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Python Igraph

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Max Greco

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0% found this document useful (0 votes)

1K views

Python Igraph

Uploaded by

Max Greco

Available Formats

Download as PDF, TXT or read online on Scribd

You are on page 1/ 429

igraph library

API Documentation
April 24, 2014

Contents
Contents

1 Package igraph
1.1 Modules . . . . . . . . .
1.2 Functions . . . . . . . .
1.3 Variables . . . . . . . .
1.4 Class Vertex . . . . . . .
1.4.1 Methods . . . . .
1.4.2 Properties . . . .
1.5 Class Graph . . . . . . .
1.5.1 Methods . . . . .
1.5.2 Properties . . . .
1.6 Class VertexSeq . . . . .
1.6.1 Methods . . . . .
1.6.2 Properties . . . .
1.7 Class EdgeSeq . . . . .
1.7.1 Methods . . . . .
1.7.2 Properties . . . .
1.8 Class ARPACKOptions
1.8.1 Methods . . . . .
1.8.2 Properties . . . .
1.9 Class BFSIter . . . . . .
1.9.1 Methods . . . . .
1.9.2 Properties . . . .
1.10 Class Edge . . . . . . .
1.10.1 Methods . . . . .
1.10.2 Properties . . . .
1.11 Class GraphBase . . . .
1.11.1 Methods . . . . .
1.11.2 Properties . . . .

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2 Module igraph._igraph
2.1 Functions . . . . . . .
2.2 Variables . . . . . . .
2.3 Class InternalError . .
2.3.1 Methods . . . .
2.3.2 Properties . . .

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3 Package igraph.app
221
3.1 Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
3.2 Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
4 Module igraph.app.shell
4.1 Functions . . . . . . . . . . . .
4.2 Variables . . . . . . . . . . . .
4.3 Class TerminalController . . . .
4.3.1 Methods . . . . . . . . .
4.3.2 Class Variables . . . . .
4.4 Class ProgressBar . . . . . . .
4.4.1 Methods . . . . . . . . .
4.4.2 Class Variables . . . . .
4.4.3 Instance Variables . . .
4.5 Class Shell . . . . . . . . . . . .
4.5.1 Methods . . . . . . . . .
4.5.2 Properties . . . . . . . .
4.6 Class IDLEShell . . . . . . . .
4.6.1 Methods . . . . . . . . .
4.6.2 Properties . . . . . . . .
4.7 Class ConsoleProgressBarMixin
4.7.1 Methods . . . . . . . . .
4.7.2 Properties . . . . . . . .
4.8 Class IPythonShell . . . . . . .
4.8.1 Methods . . . . . . . . .
4.8.2 Properties . . . . . . . .
4.9 Class ClassicPythonShell . . . .
4.9.1 Methods . . . . . . . . .
4.9.2 Properties . . . . . . . .

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5 Module igraph.clustering
5.1 Functions . . . . . . . .
5.2 Variables . . . . . . . .
5.3 Class Clustering . . . .
5.3.1 Methods . . . . .
5.3.2 Properties . . . .
5.4 Class VertexClustering .
5.4.1 Methods . . . . .
5.4.2 Properties . . . .
5.5 Class Dendrogram . . .
5.5.1 Methods . . . . .
5.5.2 Properties . . . .
5.6 Class VertexDendrogram
5.6.1 Methods . . . . .
5.6.2 Properties . . . .
5.7 Class Cover . . . . . . .
5.7.1 Methods . . . . .
5.7.2 Properties . . . .
5.8 Class VertexCover . . .
5.8.1 Methods . . . . .
5.8.2 Properties . . . .
5.9 Class CohesiveBlocks . .

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5.9.1
5.9.2

Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259

6 Module igraph.compat
260
6.1 Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
7 Module igraph.configuration
7.1 Functions . . . . . . . . . .
7.2 Variables . . . . . . . . . .
7.3 Class Configuration . . . . .
7.3.1 Methods . . . . . . .
7.3.2 Properties . . . . . .

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8 Module igraph.cut
8.1 Variables . . . .
8.2 Class Cut . . . .
8.2.1 Methods .
8.2.2 Properties
8.3 Class Flow . . . .
8.3.1 Methods .
8.3.2 Properties

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9 Module igraph.datatypes
9.1 Variables . . . . . . . . .
9.2 Class Matrix . . . . . . .
9.2.1 Methods . . . . . .
9.2.2 Properties . . . . .
9.3 Class DyadCensus . . . .
9.3.1 Methods . . . . . .
9.3.2 Properties . . . . .
9.4 Class TriadCensus . . . .
9.4.1 Methods . . . . . .
9.4.2 Properties . . . . .
9.5 Class UniqueIdGenerator
9.5.1 Methods . . . . . .
9.5.2 Properties . . . . .

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10 Package igraph.drawing
10.1 Modules . . . . . . . . . . .
10.2 Functions . . . . . . . . . .
10.3 Class DefaultGraphDrawer
10.3.1 Methods . . . . . . .
10.3.2 Properties . . . . . .
10.4 Class BoundingBox . . . . .
10.4.1 Methods . . . . . . .
10.4.2 Properties . . . . . .
10.5 Class Point . . . . . . . . .
10.5.1 Methods . . . . . . .
10.5.2 Properties . . . . . .
10.6 Class Rectangle . . . . . . .
10.6.1 Methods . . . . . . .
10.6.2 Properties . . . . . .

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10.7 Class Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301

10.7.1 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303
10.7.2 Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305
11 Module igraph.drawing.baseclasses
11.1 Variables . . . . . . . . . . . . . .
11.2 Class AbstractDrawer . . . . . . .
11.2.1 Methods . . . . . . . . . . .
11.2.2 Properties . . . . . . . . . .
11.3 Class AbstractCairoDrawer . . . .
11.3.1 Methods . . . . . . . . . . .
11.3.2 Properties . . . . . . . . . .
11.4 Class AbstractXMLRPCDrawer . .
11.4.1 Methods . . . . . . . . . . .
11.4.2 Properties . . . . . . . . . .

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12 Module igraph.drawing.colors
12.1 Functions . . . . . . . . . . . .
12.2 Variables . . . . . . . . . . . .
12.3 Class Palette . . . . . . . . . .
12.3.1 Methods . . . . . . . . .
12.3.2 Properties . . . . . . . .
12.4 Class GradientPalette . . . . .
12.4.1 Methods . . . . . . . . .
12.4.2 Properties . . . . . . . .
12.5 Class AdvancedGradientPalette
12.5.1 Methods . . . . . . . . .
12.5.2 Properties . . . . . . . .
12.6 Class RainbowPalette . . . . .
12.6.1 Methods . . . . . . . . .
12.6.2 Properties . . . . . . . .
12.7 Class PrecalculatedPalette . . .
12.7.1 Methods . . . . . . . . .
12.7.2 Properties . . . . . . . .
12.8 Class ClusterColoringPalette .
12.8.1 Methods . . . . . . . . .
12.8.2 Properties . . . . . . . .

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13 Module igraph.drawing.coord
13.1 Variables . . . . . . . . . . . . .
13.2 Class CoordinateSystem . . . . .
13.2.1 Methods . . . . . . . . . .
13.2.2 Properties . . . . . . . . .
13.3 Class DescartesCoordinateSystem
13.3.1 Methods . . . . . . . . . .
13.3.2 Properties . . . . . . . . .

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14 Module igraph.drawing.edge
14.1 Class AbstractEdgeDrawer
14.1.1 Methods . . . . . . .
14.1.2 Properties . . . . . .
14.2 Class ArrowEdgeDrawer . .

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16 Module igraph.drawing.metamagic
16.1 Class AttributeSpecification . . . .
16.1.1 Methods . . . . . . . . . . .
16.1.2 Properties . . . . . . . . . .
16.2 Class AttributeCollectorBase . . .
16.2.1 Methods . . . . . . . . . . .
16.2.2 Properties . . . . . . . . . .

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17 Module igraph.drawing.shapes
17.1 Class ShapeDrawerDirectory
17.1.1 Methods . . . . . . . .
17.1.2 Properties . . . . . . .
17.1.3 Class Variables . . . .

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18 Module igraph.drawing.text
18.1 Class TextAlignment . . . .
18.1.1 Methods . . . . . . .
18.1.2 Properties . . . . . .
18.1.3 Class Variables . . .
18.2 Class TextDrawer . . . . . .
18.2.1 Methods . . . . . . .
18.2.2 Properties . . . . . .
18.2.3 Class Variables . . .

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14.3

14.4

14.5

14.6

14.2.1 Methods . . . . . . . . .
14.2.2 Properties . . . . . . . .
Class TaperedEdgeDrawer . . .
14.3.1 Methods . . . . . . . . .
14.3.2 Properties . . . . . . . .
Class AlphaVaryingEdgeDrawer
14.4.1 Methods . . . . . . . . .
14.4.2 Properties . . . . . . . .
Class LightToDarkEdgeDrawer
14.5.1 Methods . . . . . . . . .
14.5.2 Properties . . . . . . . .
Class DarkToLightEdgeDrawer
14.6.1 Methods . . . . . . . . .
14.6.2 Properties . . . . . . . .

15 Module igraph.drawing.graph
15.1 Class DefaultGraphDrawer .
15.1.1 Methods . . . . . . . .
15.1.2 Properties . . . . . . .
15.2 Class UbiGraphDrawer . . . .
15.2.1 Methods . . . . . . . .
15.2.2 Properties . . . . . . .
15.3 Class CytoscapeGraphDrawer
15.3.1 Methods . . . . . . . .
15.3.2 Properties . . . . . . .

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19 Module igraph.drawing.utils
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19.1 Class Rectangle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353

CONTENTS

19.1.1 Methods . .
19.1.2 Properties .
19.2 Class BoundingBox
19.2.1 Methods . .
19.2.2 Properties .
19.3 Class FakeModule
19.3.1 Methods . .
19.3.2 Properties .
19.4 Class Point . . . .
19.4.1 Methods . .
19.4.2 Properties .

CONTENTS

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20 Module igraph.drawing.vertex
20.1 Class AbstractVertexDrawer . . . .
20.1.1 Methods . . . . . . . . . . .
20.1.2 Properties . . . . . . . . . .
20.2 Class AbstractCairoVertexDrawer .
20.2.1 Methods . . . . . . . . . . .
20.2.2 Properties . . . . . . . . . .
20.3 Class DefaultVertexDrawer . . . .
20.3.1 Methods . . . . . . . . . . .
20.3.2 Properties . . . . . . . . . .

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21 Module igraph.layout
21.1 Variables . . . . .
21.2 Class Layout . . .
21.2.1 Methods . .
21.2.2 Properties .

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22 Module igraph.matching
22.1 Variables . . . . . . .
22.2 Class Matching . . . .
22.2.1 Methods . . . .
22.2.2 Properties . . .

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23 Package igraph.remote
380
23.1 Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
23.2 Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
24 Module igraph.remote.gephi
24.1 Class GephiConnection . . . . . . . . . .
24.1.1 Methods . . . . . . . . . . . . . .
24.1.2 Properties . . . . . . . . . . . . .
24.2 Class GephiGraphStreamingAPIFormat
24.2.1 Methods . . . . . . . . . . . . . .
24.2.2 Properties . . . . . . . . . . . . .
24.3 Class GephiGraphStreamer . . . . . . .
24.3.1 Methods . . . . . . . . . . . . . .
24.3.2 Properties . . . . . . . . . . . . .

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25 Module igraph.remote.nexus
388
25.1 Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 388

CONTENTS

25.2 Class NexusConnection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 388

25.2.1 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389
25.2.2 Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391
26 Module igraph.statistics
26.1 Functions . . . . . . .
26.2 Class FittedPowerLaw
26.2.1 Methods . . . .
26.2.2 Properties . . .
26.3 Class Histogram . . .
26.3.1 Methods . . . .
26.3.2 Properties . . .
26.4 Class RunningMean .
26.4.1 Methods . . . .
26.4.2 Properties . . .

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27 Module igraph.summary
27.1 Class GraphSummary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
27.1.1 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
27.1.2 Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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28 Module igraph.utils
28.1 Functions . . . . . . .
28.2 Variables . . . . . . .
28.3 Class multidict . . . .
28.3.1 Methods . . . .
28.3.2 Properties . . .
28.3.3 Class Variables

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Package igraph

IGraph library.
Version: 0.7.0
License: Copyright (C) 2006-2012 Tams Nepusz <ntamas@gmail.com> Pzmny Pter stny 1/a, 1117
Budapest, Hungary
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General
Public License as published by the Free Software Foundation; either version 2 of the License, or (at your
option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See
the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write
to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA

1.1

Modules

_igraph: Low-level Python interface for the igraph library.

(Section 2, p. 216)
app: User interfaces of igraph
(Section 3, p. 221)
shell: Command-line user interface of igraph
(Section 4, p. 222)
clustering: Classes related to graph clustering.
(Section 5, p. 232)
compat: Compatibility methods and backported versions of newer Python features to enable igraph
to run on Python 2.5.
(Section 6, p. 260)
configuration: Configuration framework for igraph.
(Section 7, p. 261)
cut: Classes representing cuts and flows on graphs.
(Section 8, p. 267)
datatypes: Additional auxiliary data types
(Section 9, p. 274)
drawing: Drawing and plotting routines for IGraph.
(Section 10, p. 286)
baseclasses: Abstract base classes for the drawing routines.
(Section 11, p. 306)
colors: Color handling functions.
(Section 12, p. 310)
coord: Coordinate systems and related plotting routines
(Section 13, p. 323)
edge: Drawers for various edge styles in graph plots.
(Section 14, p. 326)
graph: Drawing routines to draw graphs.
(Section 15, p. 334)
metamagic: Auxiliary classes for the default graph drawer in igraph.
8

Modules

Package igraph

(Section 16, p. 341)

shapes: Shape drawing classes for igraph
(Section 17, p. 345)
text: Drawers for labels on plots.
(Section 18, p. 348)
utils: Utility classes for drawing routines.
(Section 19, p. 353)
vertex: Drawing routines to draw the vertices of graphs.
(Section 20, p. 364)
formula (Section ??, p. ??)
layout: Layout-related code in the IGraph library.
(Section 21, p. 369)
matching: Classes representing matchings on graphs.
(Section 22, p. 376)
remote: Classes that help igraph communicate with remote applications.
(Section 23, p. 380)
gephi: Classes that help igraph communicate with Gephi (http://www.gephi.org).
(Section 24, p. 381)
nexus: Interface to the Nexus online graph repository.
(Section 25, p. 388)
statistics: Statistics related stuff in igraph
(Section 26, p. 393)
summary (Section 1.2, p. 5)
summary: Summary representation of a graph.
(Section 27, p. 404)
utils: Utility functions that cannot be categorised anywhere else
(Section 28, p. 407)

Functions

1.2

Package igraph

Functions
autocurve(graph, attribute=curved, default=0)
Calculates curvature values for each of the edges in the graph to make sure that multiple
edges are shown properly on a graph plot.
This function checks the multiplicity of each edge in the graph and assigns curvature values
(numbers between -1 and 1, corresponding to CCW (-1), straight (0) and CW (1) curved
edges) to them. The assigned values are either stored in an edge attribute or returned as a
list, depending on the value of the attribute argument.
Parameters
graph:

the graph on which the calculation will be run

attribute: the name of the edge attribute to save the curvature values to. The
default value is curved, which is the name of the edge attribute the
default graph plotter checks to decide whether an edge should be
curved on the plot or not. If attribute is None, the result will not be
stored.
default:

the default curvature for single edges. Zero means that single edges
will be straight. If you want single edges to be curved as well, try
passing 0.5 or -0.5 here.

Return Value
the list of curvature values if attribute is None, otherwise None.
read(filename, *args, **kwds)
Loads a graph from the given filename.
This is just a convenience function, calls Graph.Read directly. All arguments are passed
unchanged to Graph.Read
Parameters
filename: the name of the file to be loaded
load(filename, *args, **kwds)
Loads a graph from the given filename.
This is just a convenience function, calls Graph.Read directly. All arguments are passed
unchanged to Graph.Read
Parameters
filename: the name of the file to be loaded
write(graph, filename, *args, **kwds)
Saves a graph to the given file.
This is just a convenience function, calls Graph.write directly. All arguments are passed
unchanged to Graph.write
Parameters
graph:

the graph to be saved

filename: the name of the file to be written

Variables

Package igraph

save(graph, filename, *args, **kwds)

Saves a graph to the given file.
This is just a convenience function, calls Graph.write directly. All arguments are passed
unchanged to Graph.write
Parameters
graph:

the graph to be saved

filename: the name of the file to be written

summary(obj, stream=None, *args, **kwds)
Prints a summary of object o to a given stream
Positional and keyword arguments not explicitly mentioned here are passed on to the
underlying summary() method of the object if it has any.
Parameters
obj:
the object about which a human-readable summary is requested.
stream: the stream to be used. If None, the standard output will be used.

1.3

Variables
Name
config
ADJ_DIRECTED
ADJ_LOWER
ADJ_MAX
ADJ_MIN
ADJ_PLUS
ADJ_UNDIRECTED
ADJ_UPPER
ALL
BLISS_F
BLISS_FL
BLISS_FLM
BLISS_FM
BLISS_FS
BLISS_FSM
GET_ADJACENCY_BOTH
GET_ADJACENCY_LOWER
GET_ADJACENCY_UPPER
IN
OUT
REWIRING_SIMPLE
REWIRING_SIMPLE_LOOPS
STAR_IN
STAR_MUTUAL
STAR_OUT

Description
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:

None
0
3
1
4
5
1
2
3
0
1
4
3
2
5
2
1

Value:
Value:
Value:
Value:
Value:

0
2
1
0
1

Value: 1
Value: 3
Value: 0
continued on next page

Class Vertex

Name
STAR_UNDIRECTED
STRONG
TRANSITIVITY_NAN
TRANSITIVITY_ZERO
TREE_IN
TREE_OUT
TREE_UNDIRECTED
WEAK
__package__
arpack_options
name

1.4

Package igraph

Description
Value: 2
Value: 2
Value: 0
Value: 1
Value: 1
Value: 0
Value: 2
Value: 1
Value: igraph
Value: <igraph.ARPACKOptions object at
0x7fc6738b8cd0>
Value: write_svg

Class Vertex

object
igraph.Vertex
Class representing a single vertex in a graph.
The vertex is referenced by its index, so if the underlying graph changes, the semantics of the vertex object
might change as well (if the vertex indices are altered in the original graph).
The attributes of the vertex can be accessed by using the vertex as a hash:
>>> v["color"] = "red"
>>> print v["color"]
red

1.4.1

#doctest: +SKIP
#doctest: +SKIP

Methods
__delitem__(x, y)
del x[y]
__eq__(x, y)
x==y
__ge__(x, y)
x>=y
__getitem__(x, y)
x[y]

Class Vertex

Package igraph

__gt__(x, y)
x>y
__hash__(x )
hash(x)
Overrides: object.__hash__
__le__(x, y)
x<=y
__len__(x )
len(x)
__lt__(x, y)
x<y
__ne__(x, y)
x!=y
__repr__(x )
repr(x)
Overrides: object.__repr__
__setitem__(x, i, y)
x[i]=y
attribute_names()
Returns the list of vertex attribute names
Return Value
list
attributes()
Returns a dict of attribute names and values for the vertex
Return Value
dict

Class Vertex

Package igraph

betweenness(...)
Proxy method to Graph.betweenness()
This method calls the betweenness method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.betweenness() for details.
closeness(...)
Proxy method to Graph.closeness()
This method calls the closeness method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.closeness() for details.
constraint(...)
Proxy method to Graph.constraint()
This method calls the constraint method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.constraint() for details.
degree(...)
Proxy method to Graph.degree()
This method calls the degree method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.degree() for details.
delete(...)
Proxy method to Graph.delete_vertices()
This method calls the delete_vertices method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.delete_vertices() for details.
diversity(...)
Proxy method to Graph.diversity()
This method calls the diversity method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.diversity() for details.

Class Vertex

Package igraph

eccentricity(...)
Proxy method to Graph.eccentricity()
This method calls the eccentricity method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.eccentricity() for details.
get_shortest_paths(...)
Proxy method to Graph.get_shortest_paths()
This method calls the get_shortest_paths method of the Graph class with this vertex as the
first argument, and returns the result.
See Also: Graph.get_shortest_paths() for details.
indegree(...)
Proxy method to Graph.indegree()
This method calls the indegree method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.indegree() for details.
is_minimal_separator(...)
Proxy method to Graph.is_minimal_separator()
This method calls the is_minimal_separator method of the Graph class with this vertex as
the first argument, and returns the result.
See Also: Graph.is_minimal_separator() for details.
is_separator(...)
Proxy method to Graph.is_separator()
This method calls the is_separator method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.is_separator() for details.
neighbors(...)
Proxy method to Graph.neighbors()
This method calls the neighbors method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.neighbors() for details.

Class Vertex

Package igraph

outdegree(...)
Proxy method to Graph.outdegree()
This method calls the outdegree method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.outdegree() for details.
pagerank(...)
Proxy method to Graph.pagerank()
This method calls the pagerank method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.pagerank() for details.
personalized_pagerank(...)
Proxy method to Graph.personalized_pagerank()
This method calls the personalized_pagerank method of the Graph class with this vertex as
the first argument, and returns the result.
See Also: Graph.personalized_pagerank() for details.
predecessors(...)
Proxy method to Graph.predecessors()
This method calls the predecessors method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.predecessors() for details.
shortest_paths(...)
Proxy method to Graph.shortest_paths()
This method calls the shortest_paths method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.shortest_paths() for details.
strength(...)
Proxy method to Graph.strength()
This method calls the strength method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.strength() for details.

Class Graph

Package igraph

successors(...)
Proxy method to Graph.successors()
This method calls the successors method of the Graph class with this vertex as the first
argument, and returns the result.
See Also: Graph.successors() for details.
update_attributes(E, **F )
Updates the attributes of the vertex from dict/iterable E and F.
If E has a keys() method, it does: for k in E: self[k] = E[k]. If E lacks a keys()
method, it does: for (k, v) in E: self[k] = v. In either case, this is followed by: for k
in F: self[k] = F[k].
This method thus behaves similarly to the update() method of Python dictionaries.
Return Value
None

Inherited from object

__delattr__(), __format__(), __getattribute__(), __init__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __str__(),
__subclasshook__()
1.4.2

Properties

Name
graph
index
Inherited from object
__class__

1.5

Description
The graph the vertex belongs to
Index of the vertex

Class Graph

object
igraph.GraphBase
igraph.Graph
Generic graph.
This class is built on top of GraphBase, so the order of the methods in the Epydoc documentation is a little bit obscure: inherited methods come after the ones implemented directly
in the subclass. Graph provides many functions that GraphBase does not, mostly because
17

Class Graph

Package igraph

these functions are not speed critical and they were easier to implement in Python than in
pure C. An example is the attribute handling in the constructor: the constructor of Graph
accepts three dictionaries corresponding to the graph, vertex and edge attributes while the
constructor of GraphBase does not. This extension was needed to make Graph serializable
through the pickle module. Graph also overrides some functions from GraphBase to provide a more convenient interface; e.g., layout functions return a Layout instance from Graph
instead of a list of coordinate pairs.
Graphs can also be indexed by strings or pairs of vertex indices or vertex names. When a
graph is indexed by a string, the operation translates to the retrieval, creation, modification
or deletion of a graph attribute:
>>>
>>>
>>>

g = Graph.Full(3)
g["name"] = "Triangle
g["name"]

graph"

Triangle graph
>>> del

g["name"]

When a graph is indexed by a pair of vertex indices or names, the graph itself is treated as
an adjacency matrix and the corresponding cell of the matrix is returned:
>>>
>>>
>>>

g = Graph.Full(3)
g.vs["name"] = ["A",
g[1, 2]

"B", "C"]

1
>>>

g["A",

"B"]

1
>>>
>>>

g["A", "B"] = 0
g.ecount()

Assigning values different from zero or one to the adjacency matrix will be translated to one,
unless the graph is weighted, in which case the numbers will be treated as weights:
>>>

g.is_weighted()

False
>>>
>>>

g["A",
g["A",

"B"]

= 2

"B"]

1
>>>
>>>

g.es["weight"] = 1.0
g.is_weighted()

True
>>>
>>>

g["A",
g["A",

"B"]

= 2

"B"]

2
>>>

g.es["weight"]

Class Graph

Package igraph

[1.0, 1.0, 2]

1.5.1

Methods

omega()
Returns the clique number of the graph.
The clique number of the graph is the size of the largest clique.
See Also: largest_cliques() for the largest cliques.
alpha()
Returns the independence number of the graph.
The independence number of the graph is the size of the largest independent
vertex set.
See Also: largest_independent_vertex_sets() for the largest independent
vertex sets
shell_index(mode=ALL)
Finds the coreness (shell index) of the vertices of the network.
The k -core of a graph is a maximal subgraph in which each vertex has at least
degree k. (Degree here means the degree in the subgraph of course). The
coreness of a vertex is k if it is a member of the k -core but not a member of
the k+1 -core.
Parameters
mode: whether to compute the in-corenesses (IN), the out-corenesses
(OUT) or the undirected corenesses (ALL). Ignored and
assumed to be ALL for undirected graphs.
Return Value
the corenesses for each vertex.
Reference: Vladimir Batagelj, Matjaz Zaversnik: An O(m) Algorithm for
Core Decomposition of Networks.
cut_vertices()
Returns the list of articulation points in the graph.
A vertex is an articulation point if its removal increases the number of
connected components in the graph.

Class Graph

Package igraph

evcent(directed =True, scale=True, weights=None, return_eigenvalue=False,

arpack_options=None)
Calculates the eigenvector centralities of the vertices in a graph.
Parameters
directed:

whether to consider edge directions in a

directed graph. Ignored for undirected graphs.

scale:

whether to normalize the centralities so the

largest one will always be 1.

weights:

edge weights given as a list or an edge

attribute. If None, all edges have equal weight.

return_eigenvalue: whether to return the actual largest

eigenvalue along with the centralities
arpack_options:

an ARPACKOptions object that can be used to

fine-tune the calculation. If it is omitted, the
module-level variable called arpack_options
is used.

Return Value
the eigenvector centralities in a list and optionally the largest
eigenvalue (as a second member of a tuple)

Class Graph

Package igraph

vertex_disjoint_paths(source=-1, target=-1, checks=True,

neighbors="error")
Calculates the vertex connectivity of the graph or between some vertices.
The vertex connectivity between two given vertices is the number of vertices
that have to be removed in order to disconnect the two vertices into two
separate components. This is also the number of vertex disjoint directed paths
between the vertices (apart from the source and target vertices of course). The
vertex connectivity of the graph is the minimal vertex connectivity over all
vertex pairs.
This method calculates the vertex connectivity of a given vertex pair if both
the source and target vertices are given. If none of them is given (or they are
both negative), the overall vertex connectivity is returned.
Parameters
source:

the source vertex involved in the calculation.

target:

the target vertex involved in the calculation.

checks:

if the whole graph connectivity is calculated and this is

True, igraph performs some basic checks before
calculation. If the graph is not strongly connected, then
the connectivity is obviously zero. If the minimum
degree is one, then the connectivity is also one. These
simple checks are much faster than checking the entire
graph, therefore it is advised to set this to True. The
parameter is ignored if the connectivity between two
given vertices is computed.

neighbors: tells igraph what to do when the two vertices are

connected. "error" raises an exception, "infinity"
returns infinity, "ignore" ignores the edge.
Return Value
the vertex connectivity

Class Graph

Package igraph

edge_disjoint_paths(source=-1, target=-1, checks=True)

Calculates the edge connectivity of the graph or between some vertices.
The edge connectivity between two given vertices is the number of edges that
have to be removed in order to disconnect the two vertices into two separate
components. This is also the number of edge disjoint directed paths between
the vertices. The edge connectivity of the graph is the minimal edge
connectivity over all vertex pairs.
This method calculates the edge connectivity of a given vertex pair if both the
source and target vertices are given. If none of them is given (or they are both
negative), the overall edge connectivity is returned.
Parameters
source: the source vertex involved in the calculation.
target: the target vertex involved in the calculation.
checks: if the whole graph connectivity is calculated and this is
True, igraph performs some basic checks before calculation.
If the graph is not strongly connected, then the
connectivity is obviously zero. If the minimum degree is
one, then the connectivity is also one. These simple checks
are much faster than checking the entire graph, therefore it
is advised to set this to True. The parameter is ignored if
the connectivity between two given vertices is computed.
Return Value
the edge connectivity

Class Graph

Package igraph

cohesion(source=-1, target=-1, checks=True, neighbors="error")

Calculates the vertex connectivity of the graph or between some vertices.
The vertex connectivity between two given vertices is the number of vertices
that have to be removed in order to disconnect the two vertices into two
separate components. This is also the number of vertex disjoint directed paths
between the vertices (apart from the source and target vertices of course). The
vertex connectivity of the graph is the minimal vertex connectivity over all
vertex pairs.
This method calculates the vertex connectivity of a given vertex pair if both
the source and target vertices are given. If none of them is given (or they are
both negative), the overall vertex connectivity is returned.
Parameters
source:

the source vertex involved in the calculation.

target:

the target vertex involved in the calculation.

checks:

if the whole graph connectivity is calculated and this is

neighbors: tells igraph what to do when the two vertices are

connected. "error" raises an exception, "infinity"
returns infinity, "ignore" ignores the edge.
Return Value
the vertex connectivity

Class Graph

Package igraph

adhesion(source=-1, target=-1, checks=True)

Class Graph

Package igraph

shortest_paths_dijkstra(source=None, target=None, weights=None,

mode=OUT)
Calculates shortest path lengths for given vertices in a graph.
The algorithm used for the calculations is selected automatically: a simple
BFS is used for unweighted graphs, Dijkstras algorithm is used when all the
weights are positive. Otherwise, the Bellman-Ford algorithm is used if the
number of requested source vertices is larger than 100 and Johnsons algorithm
is used otherwise.
Parameters
source: a list containing the source vertex IDs which should be
included in the result. If None, all vertices will be
considered.
target: a list containing the target vertex IDs which should be
included in the result. If None, all vertices will be
considered.
weights: a list containing the edge weights. It can also be an
attribute name (edge weights are retrieved from the given
attribute) or None (all edges have equal weight).
mode:

the type of shortest paths to be used for the calculation in

directed graphs. OUT means only outgoing, IN means only
incoming paths. ALL means to consider the directed graph
as an undirected one.

Return Value
the shortest path lengths for given vertices in a matrix

Class Graph

Package igraph

subgraph(vertices, implementation="auto")
Returns a subgraph spanned by the given vertices.
Parameters
vertices:

a list containing the vertex IDs which should be

included in the result.

implementation: the implementation to use when constructing the

new subgraph. igraph includes two
implementations at the moment.
"copy_and_delete" copies the original graph and
removes those vertices that are not in the given
set. This is more efficient if the size of the
subgraph is comparable to the original graph. The
other implementation ("create_from_scratch")
constructs the result graph from scratch and then
copies the attributes accordingly. This is a better
solution if the subgraph is relatively small,
compared to the original graph. "auto" selects
between the two implementations automatically,
based on the ratio of the size of the subgraph and
the size of the original graph.
Return Value
the subgraph

Class Graph

Package igraph

init(n=None, edges=None, directed =None, graph_attrs=None,

vertex_attrs=None, edge_attrs=None)
Constructs a graph from scratch.
Parameters
n:

the number of vertices. Can be omitted, the default

is zero.

edges:

the edge list where every list item is a pair of

integers. If any of the integers is larger than n-1, the
number of vertices is adjusted accordingly.

directed:

whether the graph should be directed

graph_attrs: the attributes of the graph as a dictionary.

vertex_attrs: the attributes of the vertices as a dictionary. Every
dictionary value must be an iterable with exactly n
items.
edge_attrs:

the attributes of the edges as a dictionary. Every

dictionary value must be an iterable with exactly m
items where m is the number of edges.

Overrides: object.__init__
add_edge(source, target, **kwds)
Adds a single edge to the graph.
Keyword arguments (except the source and target arguments) will be assigned
to the edge as attributes.
Parameters
source: the source vertex of the edge or its name.
target: the target vertex of the edge or its name.
add_edges(es)
Adds some edges to the graph.
Parameters
es: the list of edges to be added. Every edge is represented with a
tuple containing the vertex IDs or names of the two endpoints.
Vertices are enumerated from zero.
Overrides: igraph.GraphBase.add_edges

Class Graph

Package igraph

add_vertex(name=None, **kwds)
Adds a single vertex to the graph. Keyword arguments will be assigned as
vertex attributes. Note that name as a keyword argument is treated specially;
if a graph has name as a vertex attribute, it allows one to refer to vertices by
their names in most places where igraph expects a vertex ID.
add_vertices(n)
Adds some vertices to the graph.
Parameters
n: the number of vertices to be added, or the name of a single vertex
to be added, or an iterable of strings, each corresponding to the
name of a vertex to be added. Names will be assigned to the
name vertex attribute.
Overrides: igraph.GraphBase.add_vertices
adjacent(vertex, mode=OUT)
Returns the edges a given vertex is incident on.
Deprecated: replaced by Graph.incident() since igraph 0.6
as_directed(*args, **kwds)
Returns a directed copy of this graph. Arguments are passed on to
Graph.to_directed() that is invoked on the copy.
as_undirected(*args, **kwds)
Returns an undirected copy of this graph. Arguments are passed on to
Graph.to_undirected() that is invoked on the copy.

Class Graph

Package igraph

delete_edges(self, *args, **kwds)

Deletes some edges from the graph.
The set of edges to be deleted is determined by the positional and keyword
arguments. If any keyword argument is present, or the first positional
argument is callable, an edge sequence is derived by calling EdgeSeq.select
with the same positional and keyword arguments. Edges in the derived edge
sequence will be removed. Otherwise the first positional argument is
considered as follows:

None - deletes all edges

a single integer - deletes the edge with the given ID
a list of integers - deletes the edges denoted by the given IDs
a list of 2-tuples - deletes the edges denoted by the given source-target
vertex pairs. When multiple edges are present between a given
source-target vertex pair, only one is removed.

Parameters
es: the list of edges to be removed. Edges are identifed by edge IDs.
EdgeSeq objects are also accepted here.
Overrides: igraph.GraphBase.delete_edges
indegree(self, *args, **kwds)
Returns the in-degrees in a list.
See degree for possible arguments.
outdegree(self, *args, **kwds)
Returns the out-degrees in a list.
See degree for possible arguments.

Class Graph

Package igraph

all_st_cuts(self, source, target)

Returns all the cuts between the source and target vertices in a directed graph.
This function lists all edge-cuts between a source and a target vertex. Every
cut is listed exactly once.
Parameters
source: the source vertex ID
target: the target vertex ID
Return Value
a list of Cut objects.
Overrides: igraph.GraphBase.all_st_cuts
Reference: JS Provan and DR Shier: A paradigm for listing (s,t)-cuts in
graphs. Algorithmica 15, 351372, 1996.
all_st_mincuts(self, source, target, capacity=None)
Returns all the mincuts between the source and target vertices in a directed
graph.
This function lists all minimum edge-cuts between a source and a target vertex.
Parameters
source:

the source vertex ID

target:

the target vertex ID

capacity: the edge capacities (weights). If None, all edges have

equal weight. May also be an attribute name.
Return Value
a list of Cut objects.
Overrides: igraph.GraphBase.all_st_mincuts
Reference: JS Provan and DR Shier: A paradigm for listing (s,t)-cuts in
graphs. Algorithmica 15, 351372, 1996.

Class Graph

Package igraph

biconnected_components(self, return_articulation_points=False)
Calculates the biconnected components of the graph.
Parameters
return_articulation_points: whether to return the articulation
points as well
Return Value
a VertexCover object describing the biconnected components, and
optionally the list of articulation points as well
Overrides: igraph.GraphBase.biconnected_components
blocks(self, return_articulation_points=False)
Calculates the biconnected components of the graph.
Parameters
return_articulation_points: whether to return the articulation
points as well
Return Value
a VertexCover object describing the biconnected components, and
optionally the list of articulation points as well
cohesive_blocks()
Calculates the cohesive block structure of the graph.
Cohesive blocking is a method of determining hierarchical subsets of graph
vertices based on their structural cohesion (i.e. vertex connectivity). For a
given graph G, a subset of its vertices S is said to be maximally k-cohesive if
there is no superset of S with vertex connectivity greater than or equal to k.
Cohesive blocking is a process through which, given a k-cohesive set of
vertices, maximally l-cohesive subsets are recursively identified with l > k.
Thus a hierarchy of vertex subsets is obtained in the end, with the entire
graph G at its root.
Return Value
an instance of CohesiveBlocks. See the documentation of
CohesiveBlocks for more information.
Overrides: igraph.GraphBase.cohesive_blocks
See Also: CohesiveBlocks

Class Graph

Package igraph

clusters(mode=STRONG)
Calculates the (strong or weak) clusters (connected components) for a given
graph.
Parameters
mode: must be either STRONG or WEAK, depending on the clusters
being sought. Optional, defaults to STRONG.
Return Value
a VertexClustering object
Overrides: igraph.GraphBase.clusters
components(mode=STRONG)
Calculates the (strong or weak) clusters (connected components) for a given
graph.
Parameters
mode: must be either STRONG or WEAK, depending on the clusters
being sought. Optional, defaults to STRONG.
Return Value
a VertexClustering object
degree_distribution(bin_width=1, ...)
Calculates the degree distribution of the graph.
Unknown keyword arguments are directly passed to degree().
Parameters
bin_width: the bin width of the histogram
Return Value
a histogram representing the degree distribution of the graph.

Class Graph

Package igraph

dyad_census()
Calculates the dyad census of the graph.
Dyad census means classifying each pair of vertices of a directed graph into
three categories: mutual (there is an edge from a to b and also from b to a),
asymmetric (there is an edge from a to b or from b to a but not the other way
round) and null (there is no connection between a and b).
Return Value
a DyadCensus object.
Overrides: igraph.GraphBase.dyad_census
Reference: Holland, P.W. and Leinhardt, S. (1970). A Method for Detecting
Structure in Sociometric Data. American Journal of Sociology, 70, 492-513.
get_adjacency(self, type=2, attribute=None, default=0, eids=False)
Returns the adjacency matrix of a graph.
Parameters
type:

either GET_ADJACENCY_LOWER (uses the lower triangle of

the matrix) or GET_ADJACENCY_UPPER (uses the upper
triangle) or GET_ADJACENCY_BOTH (uses both parts).
Ignored for directed graphs.

attribute: if None, returns the ordinary adjacency matrix. When

the name of a valid edge attribute is given here, the
matrix returned will contain the default value at the
places where there is no edge or the value of the given
attribute where there is an edge. Multiple edges are not
supported, the value written in the matrix in this case
will be unpredictable. This parameter is ignored if eids
is True
default:

the default value written to the cells in the case of

adjacency matrices with attributes.

eids:

specifies whether the edge IDs should be returned in the

adjacency matrix. Since zero is a valid edge ID, the
cells in the matrix that correspond to unconnected
vertex pairs will contain -1 instead of 0 if eids is True.
If eids is False, the number of edges will be returned in
the matrix for each vertex pair.

Return Value
the adjacency matrix as a Matrix.
Overrides: igraph.GraphBase.get_adjacency

Class Graph

Package igraph

get_adjlist(mode=OUT)
Returns the adjacency list representation of the graph.
The adjacency list representation is a list of lists. Each item of the outer list
belongs to a single vertex of the graph. The inner list contains the neighbors
of the given vertex.
Parameters
mode: if OUT, returns the successors of the vertex. If IN, returns the
predecessors of the vertex. If ALL, both the predecessors and
the successors will be returned. Ignored for undirected graphs.
get_adjedgelist(mode=OUT)
Returns the incidence list representation of the graph.
Deprecated: replaced by Graph.get_inclist() since igraph 0.6
See Also: Graph.get_inclist()
get_inclist(mode=OUT)
Returns the incidence list representation of the graph.
The incidence list representation is a list of lists. Each item of the outer list
belongs to a single vertex of the graph. The inner list contains the IDs of the
incident edges of the given vertex.
Parameters
mode: if OUT, returns the successors of the vertex. If IN, returns the
predecessors of the vertex. If ALL, both the predecessors and
the successors will be returned. Ignored for undirected graphs.

Class Graph

Package igraph

gomory_hu_tree(capacity=None, flow ="flow")

Calculates the Gomory-Hu tree of an undirected graph with optional edge
capacities.
The Gomory-Hu tree is a concise representation of the value of all the
maximum flows (or minimum cuts) in a graph. The vertices of the tree
correspond exactly to the vertices of the original graph in the same order.
Edges of the Gomory-Hu tree are annotated by flow values. The value of the
maximum flow (or minimum cut) between an arbitrary (u,v) vertex pair in the
original graph is then given by the minimum flow value (i.e. edge annotation)
along the shortest path between u and v in the Gomory-Hu tree.
Parameters
capacity: the edge capacities (weights). If None, all edges have
equal weight. May also be an attribute name.
flow:

the name of the edge attribute in the returned graph in

which the flow values will be stored.

Return Value
the Gomory-Hu tree as a Graph object.
Overrides: igraph.GraphBase.gomory_hu_tree
is_named()
Returns whether the graph is named, i.e. whether it has a "name" vertex
attribute.
is_weighted()
Returns whether the graph is weighted, i.e. whether it has a "weight" edge
attribute.

Class Graph

Package igraph

maxflow(source, target, capacity=None)

Returns a maximum flow between the given source and target vertices in a
graph.
A maximum flow from source to target is an assignment of non-negative real
numbers to the edges of the graph, satisfying two properties:
1. For each edge, the flow (i.e. the assigned number) is not more than the
capacity of the edge (see the capacity argument)
2. For every vertex except the source and the target, the incoming flow is
the same as the outgoing flow.
The value of the flow is the incoming flow of the target or the outgoing flow of
the source (which are equal). The maximum flow is the maximum possible
such value.
Parameters
capacity: the edge capacities (weights). If None, all edges have
equal weight. May also be an attribute name.
Return Value
a Flow object describing the maximum flow
Overrides: igraph.GraphBase.maxflow

Class Graph

Package igraph

mincut(source=None, target=None, capacity=None)

Calculates the minimum cut between the given source and target vertices or
within the whole graph.
The minimum cut is the minimum set of edges that needs to be removed to
separate the source and the target (if they are given) or to disconnect the
graph (if neither the source nor the target are given). The minimum is
calculated using the weights (capacities) of the edges, so the cut with the
minimum total capacity is calculated.
For undirected graphs and no source and target, the method uses the
Stoer-Wagner algorithm. For a given source and target, the method uses the
push-relabel algorithm; see the references below.
Parameters
source:

target:

the source vertex ID. If None, the target must also be

None and the calculation will be done for the entire
graph (i.e. all possible vertex pairs).
the target vertex ID. If None, the source must also be
None and the calculation will be done for the entire
graph (i.e. all possible vertex pairs).

capacity: the edge capacities (weights). If None, all edges have

equal weight. May also be an attribute name.
Return Value
a Cut object describing the minimum cut
Overrides: igraph.GraphBase.mincut
st_mincut(source, target, capacity=None)
Calculates the minimum cut between the source and target vertices in a graph.
Parameters
source:

the source vertex ID

target:

the target vertex ID

capacity: the capacity of the edges. It must be a list or a valid

Class Graph

Package igraph

modularity(membership, weights=None)
Calculates the modularity score of the graph with respect to a given clustering.
The modularity of a graph w.r.t. some division measures how good the
division is, or how separated are the different vertex types from each other.
Its defined as Q=1/(2m)*sum(Aij-ki*kj/(2m)delta(ci,cj),i,j). m is the number
of edges, Aij is the element of the A adjacency matrix in row i and column j,
ki is the degree of node i, kj is the degree of node j, and Ci and cj are the
types of the two vertices (i and j ). delta(x,y) is one iff x=y, 0 otherwise.
If edge weights are given, the definition of modularity is modified as follows:
Aij becomes the weight of the corresponding edge, ki is the total weight of
edges adjacent to vertex i, kj is the total weight of edges adjacent to vertex j
and m is the total edge weight in the graph.
Parameters
membership: a membership list or a VertexClustering object
weights:

optional edge weights or None if all edges are weighed

equally. Attribute names are also allowed.

Return Value
the modularity score
Overrides: igraph.GraphBase.modularity
Reference: MEJ Newman and M Girvan: Finding and evaluating community
structure in networks. Phys Rev E 69 026113, 2004.
path_length_hist(directed =True)
Returns the path length histogram of the graph
Parameters
directed: whether to consider directed paths. Ignored for
undirected graphs.
Return Value
a Histogram object. The object will also have an unconnected
attribute that stores the number of unconnected vertex pairs (where
the second vertex can not be reached from the first one). The latter
one will be of type long (and not a simple integer), since this can be
very large.
Overrides: igraph.GraphBase.path_length_hist

Class Graph

Package igraph

pagerank(self, vertices=None, directed =True, damping=0.85, weights=None,

arpack_options=None, implementation=prpack, niter =1000, eps=0.001)
Calculates the Google PageRank values of a graph.
Parameters
vertices:

the indices of the vertices being queried. None

means all of the vertices.

directed:

whether to consider directed paths.

damping:

the damping factor. 1-damping is the PageRank

value for nodes with no incoming links. It is also
the probability of resetting the random walk to a
uniform distribution in each step.

weights:

edge weights to be used. Can be a sequence or

iterable or even an edge attribute name.

arpack_options: an ARPACKOptions object used to fine-tune the

ARPACK eigenvector calculation. If omitted, the
module-level variable called arpack_options is
used. This argument is ignored if not the
ARPACK implementation is used, see the
implementation argument.
implementation: which implementation to use to solve the
PageRank eigenproblem. Possible values are:
"prpack": use the PRPACK library. This is a
new implementation in igraph 0.7
"arpack": use the ARPACK library. This
implementation was used from version 0.5,
until version 0.7.
"power": use a simple power method. This is
the implementation that was used before
igraph version 0.5.
niter:

The number of iterations to use in the power

method implementation. It is ignored in the other
implementations

eps:

The power method implementation will consider

the calculation as complete if the difference of
PageRank values between iterations change less
than this value for every node. It is ignored by
the other implementations.

Return Value
a list with the Google PageRank values of the specified vertices.

Class Graph

Package igraph

spanning_tree(self, weights=None, return_tree=True)

Calculates a minimum spanning tree for a graph.
Parameters
weights:

a vector containing weights for every edge in the

graph. None means that the graph is unweighted.

return_tree: whether to return the minimum spanning tree (when

return_tree is True) or to return the IDs of the
edges in the minimum spanning tree instead (when
return_tree is False). The default is True for
historical reasons as this argument was introduced in
igraph 0.6.
Return Value
the spanning tree as a Graph object if return_tree is True or the
IDs of the edges that constitute the spanning tree if return_tree is
False.
Reference: Prim, R.C.: Shortest connection networks and some
generalizations. Bell System Technical Journal 36:1389-1401, 1957.

Class Graph

Package igraph

transitivity_avglocal_undirected(self, mode=nan, weights=None)

Calculates the average of the vertex transitivities of the graph.
In the unweighted case, the transitivity measures the probability that two
neighbors of a vertex are connected. In case of the average local transitivity,
this probability is calculated for each vertex and then the average is taken.
Vertices with less than two neighbors require special treatment, they will
either be left out from the calculation or they will be considered as having zero
transitivity, depending on the mode parameter. The calculation is slightly
more involved for weighted graphs; in this case, weights are taken into account
according to the formula of Barrat et al (see the references).
Note that this measure is different from the global transitivity measure (see
transitivity_undirected()) as it simply takes the average local transitivity
across the whole network.
Parameters
mode:

defines how to treat vertices with degree less than two. If

TRANSITIVITY_ZERO or "zero", these vertices will have
zero transitivity. If TRANSITIVITY_NAN or "nan", these
vertices will be excluded from the average.

weights: edge weights to be used. Can be a sequence or iterable or

even an edge attribute name.
Overrides: igraph.GraphBase.transitivity_avglocal_undirected
See Also: transitivity_undirected(),
transitivity_local_undirected()
Reference:
Watts DJ and Strogatz S: Collective dynamics of small-world
networks. Nature 393(6884):440-442, 1998.
Barrat A, Barthelemy M, Pastor-Satorras R and Vespignani A:
The architecture of complex weighted networks. PNAS 101, 3747
(2004). http://arxiv.org/abs/cond-mat/0311416 .
triad_census()
Calculates the triad census of the graph.
Return Value
a TriadCensus object.
Overrides: igraph.GraphBase.triad_census
Reference: Davis, J.A. and Leinhardt, S. (1972). The Structure of Positive
Interpersonal Relations in Small Groups. In: J. Berger (Ed.), Sociological
Theories in Progress, Volume 2, 218-251. Boston: Houghton Mifflin.
41

Class Graph

Package igraph

count_automorphisms_vf2(self, color =None, edge_color =None,

node_compat_fn=None, edge_compat_fn=None)
Returns the number of automorphisms of the graph.
This function simply calls count_isomorphisms_vf2 with the graph itself. See
count_isomorphisms_vf2 for an explanation of the parameters.
Return Value
the number of automorphisms of the graph
See Also: Graph.count_isomorphisms_vf2
get_automorphisms_vf2(self, color =None, edge_color =None,
node_compat_fn=None, edge_compat_fn=None)
Returns all the automorphisms of the graph
This function simply calls get_isomorphisms_vf2 with the graph itself. See
get_isomorphisms_vf2 for an explanation of the parameters.
Return Value
a list of lists, each item containing a possible mapping of the graph
vertices to itself according to the automorphism
See Also: Graph.get_isomorphisms_vf2
community_fastgreedy(self, weights=None)
Community structure based on the greedy optimization of modularity.
This algorithm merges individual nodes into communities in a way that
greedily maximizes the modularity score of the graph. It can be proven that if
no merge can increase the current modularity score, the algorithm can be
stopped since no further increase can be achieved.
This algorithm is said to run almost in linear time on sparse graphs.
Parameters
weights: edge attribute name or a list containing edge weights
Return Value
an appropriate VertexDendrogram object.
Overrides: igraph.GraphBase.community_fastgreedy
Reference: A Clauset, MEJ Newman and C Moore: Finding community
structure in very large networks. Phys Rev E 70, 066111 (2004).

Class Graph

Package igraph

community_infomap(self, edge_weights=None, vertex_weights=None,

trials=10)
Finds the community structure of the network according to the Infomap
method of Martin Rosvall and Carl T. Bergstrom.
Parameters
edge_weights:

name of an edge attribute or a list containing

edge weights.

vertex_weights: name of an vertex attribute or a list containing

vertex weights.
trials:

the number of attempts to partition the network.

Return Value
an appropriate VertexClustering object with an extra attribute
called codelength that stores the code length determined by the
algorithm.
Overrides: igraph.GraphBase.community_infomap
Reference:
M. Rosvall and C. T. Bergstrom: Maps of information flow
reveal community structure in complex networks, PNAS 105,
1118 (2008). http://dx.doi.org/10.1073/pnas.0706851105 ,
http://arxiv.org/abs/0707.0609 .
M. Rosvall, D. Axelsson, and C. T. Bergstrom: The map
equation, Eur. Phys. J. Special Topics 178, 13 (2009).
http://dx.doi.org/10.1140/epjst/e2010-01179-1 ,
http://arxiv.org/abs/0906.1405 .

Class Graph

Package igraph

community_leading_eigenvector_naive(clusters=None,
return_merges=False)
A naive implementation of Newmans eigenvector community structure
detection. This function splits the network into two components according to
the leading eigenvector of the modularity matrix and then recursively takes
the given number of steps by splitting the communities as individual networks.
This is not the correct way, however, see the reference for explanation.
Consider using the correct community_leading_eigenvector method instead.
Parameters
clusters:

the desired number of communities. If None, the

algorithm tries to do as many splits as possible.
Note that the algorithm wont split a community
further if the signs of the leading eigenvector are
all the same, so the actual number of discovered
communities can be less than the desired one.

return_merges: whether the returned object should be a

dendrogram instead of a single clustering.
Return Value
an appropriate VertexClustering or VertexDendrogram object.
Reference: MEJ Newman: Finding community structure in networks using
the eigenvectors of matrices, arXiv:physics/0605087

Class Graph

Package igraph

community_leading_eigenvector(clusters=None, weights=None,
arpack_options=None)
Newmans leading eigenvector method for detecting community structure.
This is the proper implementation of the recursive, divisive algorithm: each
split is done by maximizing the modularity regarding the original network.
Parameters
clusters:

weights:

the desired number of communities. If None, the

arpack_options: an ARPACKOptions object used to fine-tune the

ARPACK eigenvector calculation. If omitted, the
module-level variable called arpack_options is
used.
Return Value
an appropriate VertexClustering object.
Overrides: igraph.GraphBase.community_leading_eigenvector
Reference: MEJ Newman: Finding community structure in networks using
the eigenvectors of matrices, arXiv:physics/0605087

Class Graph

Package igraph

community_label_propagation(weights=None, initial =None, fixed =None)

Finds the community structure of the graph according to the label propagation
method of Raghavan et al. Initially, each vertex is assigned a different label.
After that, each vertex chooses the dominant label in its neighbourhood in
each iteration. Ties are broken randomly and the order in which the vertices
are updated is randomized before every iteration. The algorithm ends when
vertices reach a consensus. Note that since ties are broken randomly, there is
no guarantee that the algorithm returns the same community structure after
each run. In fact, they frequently differ. See the paper of Raghavan et al on
how to come up with an aggregated community structure.
Parameters
weights: name of an edge attribute or a list containing edge weights
initial: name of a vertex attribute or a list containing the initial
vertex labels. Labels are identified by integers from zero
to n-1 where n is the number of vertices. Negative
numbers may also be present in this vector, they represent
unlabeled vertices.
fixed:

a list of booleans for each vertex. True corresponds to

vertices whose labeling should not change during the
algorithm. It only makes sense if initial labels are also
given. Unlabeled vertices cannot be fixed.

Return Value
an appropriate VertexClustering object.
Overrides: igraph.GraphBase.community_label_propagation
Reference: Raghavan, U.N. and Albert, R. and Kumara, S. Near linear time
algorithm to detect community structures in large-scale networks. Phys Rev E
76:036106, 2007. http://arxiv.org/abs/0709.2938 .

Class Graph

Package igraph

community_multilevel(self, weights=None, return_levels=False)

Community structure based on the multilevel algorithm of Blondel et al.
This is a bottom-up algorithm: initially every vertex belongs to a separate
community, and vertices are moved between communities iteratively in a way
that maximizes the vertices local contribution to the overall modularity score.
When a consensus is reached (i.e. no single move would increase the
modularity score), every community in the original graph is shrank to a single
vertex (while keeping the total weight of the adjacent edges) and the process
continues on the next level. The algorithm stops when it is not possible to
increase the modularity any more after shrinking the communities to vertices.
This algorithm is said to run almost in linear time on sparse graphs.
Parameters
weights:

edge attribute name or a list containing edge

weights

return_levels: if True, the communities at each level are returned

in a list. If False, only the community structure
with the best modularity is returned.
Return Value
a list of VertexClustering objects, one corresponding to each level
(if return_levels is True), or a VertexClustering corresponding
to the best modularity.
Overrides: igraph.GraphBase.community_multilevel
Reference: VD Blondel, J-L Guillaume, R Lambiotte and E Lefebvre: Fast
unfolding of community hierarchies in large networks, J Stat Mech P10008
(2008), http://arxiv.org/abs/0803.0476

Class Graph

Package igraph

community_optimal_modularity(self, *args, **kwds)

Calculates the optimal modularity score of the graph and the corresponding
community structure.
This function uses the GNU Linear Programming Kit to solve a large integer
optimization problem in order to find the optimal modularity score and the
corresponding community structure, therefore it is unlikely to work for graphs
larger than a few (less than a hundred) vertices. Consider using one of the
heuristic approaches instead if you have such a large graph.
Parameters
weights: name of an edge attribute or a list containing edge
weights.
Return Value
the calculated membership vector and the corresponding modularity
in a tuple.
Overrides: igraph.GraphBase.community_optimal_modularity

Class Graph

Package igraph

community_edge_betweenness(self, clusters=None, directed =True,

weights=None)
Community structure based on the betweenness of the edges in the network.
The idea is that the betweenness of the edges connecting two communities is
typically high, as many of the shortest paths between nodes in separate
communities go through them. So we gradually remove the edge with the
highest betweenness and recalculate the betweennesses after every removal.
This way sooner or later the network falls of to separate components. The
result of the clustering will be represented by a dendrogram.
Parameters
clusters: the number of clusters we would like to see. This
practically defines the "level" where we "cut" the
dendrogram to get the membership vector of the vertices.
If None, the dendrogram is cut at the level which
maximizes the modularity.
directed: whether the directionality of the edges should be taken
into account or not.
weights: name of an edge attribute or a list containing edge
weights.
Return Value
a VertexDendrogram object, initally cut at the maximum
modularity or at the desired number of clusters.
Overrides: igraph.GraphBase.community_edge_betweenness

Class Graph

Package igraph

community_spinglass(weights=None, spins=25, parupdate=False,

start_temp=1, stop_temp=0.01, cool_fact=0.99, update_rule="config",
gamma=1, implementation="orig", lambda_=1)
Finds the community structure of the graph according to the spinglass
community detection method of Reichardt & Bornholdt.
Parameters
weights:

edge weights to be used. Can be a sequence or

iterable or even an edge attribute name.

spins:

integer, the number of spins to use. This is the

upper limit for the number of communities. It is
not a problem to supply a (reasonably) big
number here, in which case some spin states will
be unpopulated.

parupdate:

whether to update the spins of the vertices in

parallel (synchronously) or not

start_temp:

the starting temperature

stop_temp:

the stop temperature

cool_fact:

cooling factor for the simulated annealing

update_rule:

specifies the null model of the simulation.

Possible values are "config" (a random graph
with the same vertex degrees as the input graph)
or "simple" (a random graph with the same
number of edges)

gamma:

the gamma argument of the algorithm, specifying

the balance between the importance of present
and missing edges within a community. The
default value of 1.0 assigns equal importance to
both of them.

implementation: currently igraph contains two implementations of

the spinglass community detection algorithm.
The faster original implementation is the default.
The other implementation is able to take into
account negative weights, this can be chosen by
setting implementation to "neg"
lambda_:

the lambda argument of the algorithm, which

specifies the balance between the importance of
present and missing negatively weighted edges
within a community. Smaller values of lambda
lead to communities with less negative
intra-connectivity. If the argument is zero, the
algorithm reduces to a graph coloring algorithm,
using the number
of spins as colors. This
50
argument is ignored if the original
implementation is used. Note the underscore at
the end of the argument name; this is due to the
fact that lambda is a reserved keyword in Python.

Class Graph

Package igraph

community_walktrap(self, weights=None, steps=4)

Community detection algorithm of Latapy & Pons, based on random walks.
The basic idea of the algorithm is that short random walks tend to stay in the
same community. The result of the clustering will be represented as a
dendrogram.
Parameters
weights: name of an edge attribute or a list containing edge weights
steps:

length of random walks to perform

Return Value
a VertexDendrogram object, initially cut at the maximum
modularity.
Overrides: igraph.GraphBase.community_walktrap
Reference: Pascal Pons, Matthieu Latapy: Computing communities in large
networks using random walks, http://arxiv.org/abs/physics/0512106 .
k_core(self, *args)
Returns some k-cores of the graph.
The method accepts an arbitrary number of arguments representing the
desired indices of the k -cores to be returned. The arguments can also be lists
or tuples. The result is a single Graph object if an only integer argument was
given, otherwise the result is a list of Graph objects representing the desired
k-cores in the order the arguments were specified. If no argument is given,
returns all k -cores in increasing order of k.

Class Graph

Package igraph

layout(self, layout=None, *args, **kwds)

Returns the layout of the graph according to a layout algorithm.
Parameters and keyword arguments not specified here are passed to the layout
algorithm directly. See the documentation of the layout algorithms for the
explanation of these parameters.
Registered layout names understood by this method are:

auto, automatic: automatic layout (see Graph.layout_auto)

bipartite: bipartite layout (see Graph.layout_bipartite)
circle, circular: circular layout (see Graph.layout_circle)
drl: DrL layout for large graphs (see Graph.layout_drl)
drl_3d: 3D DrL layout for large graphs (see Graph.layout_drl)
fr, fruchterman_reingold: Fruchterman-Reingold layout (see
Graph.layout_fruchterman_reingold).
fr_3d, fr3d, fruchterman_reingold_3d: 3D Fruchterman- Reingold
layout (see Graph.layout_fruchterman_reingold).
grid: regular grid layout in 2D (see Graph.layout_grid)
grid_3d: regular grid layout in 3D (see Graph.layout_grid_3d)
graphopt: the graphopt algorithm (see Graph.layout_graphopt)
gfr, grid_fr, grid_fruchterman_reingold: grid-based
Fruchterman-Reingold layout (see
Graph.layout_grid_fruchterman_reingold)
kk, kamada_kawai: Kamada-Kawai layout (see
Graph.layout_kamada_kawai)
kk_3d, kk3d, kamada_kawai_3d: 3D Kamada-Kawai layout (see
Graph.layout_kamada_kawai)
lgl, large, large_graph: Large Graph Layout (see Graph.layout_lgl)
mds: multidimensional scaling layout (see Graph.layout_mds)
random: random layout (see Graph.layout_random)
random_3d: random 3D layout (see Graph.layout_random)
rt, tree, reingold_tilford: Reingold-Tilford tree layout (see
Graph.layout_reingold_tilford)
rt_circular, reingold_tilford_circular: circular Reingold-Tilford
tree layout (see Graph.layout_reingold_tilford_circular)
sphere, spherical, circle_3d, circular_3d: spherical layout (see
Graph.layout_circle)
star: star layout (see Graph.layout_star)
sugiyama: Sugiyama layout (see Graph.layout_sugiyama)

Parameters
52 be one of the registered layout
layout: the layout to use. This can
names or a callable which returns either a Layout object or
a list of lists containing the coordinates. If None, uses the
value of the plotting.layout configuration key.

Class Graph

Package igraph

layout_auto(self, *args, **kwds)

Chooses and runs a suitable layout function based on simple topological
properties of the graph.
This function tries to choose an appropriate layout function for the graph
using the following rules:
1. If the graph has an attribute called layout, it will be used. It may either
be a Layout instance, a list of coordinate pairs, the name of a layout
function, or a callable function which generates the layout when called
with the graph as a parameter.
2. Otherwise, if the graph has vertex attributes called x and y, these will be
used as coordinates in the layout. When a 3D layout is requested (by
setting dim to 3), a vertex attribute named z will also be needed.
3. Otherwise, if the graph is connected and has at most 100 vertices, the
Kamada-Kawai layout will be used (see Graph.layout_kamada_kawai()).
4. Otherwise, if the graph has at most 1000 vertices, the
Fruchterman-Reingold layout will be used (see
Graph.layout_fruchterman_reingold()).
5. If everything else above failed, the DrL layout algorithm will be used (see
Graph.layout_drl()).
All the arguments of this function except dim are passed on to the chosen
layout function (in case we have to call some layout function).
Parameters
dim: specifies whether we would like to obtain a 2D or a 3D layout.
Return Value
a Layout object.

Class Graph

Package igraph

layout_sugiyama(layers=None, weights=None, hgap=1, vgap=1,

maxiter =100, return_extended_graph=False)
Places the vertices using a layered Sugiyama layout.
This is a layered layout that is most suitable for directed acyclic graphs,
although it works on undirected or cyclic graphs as well.
Each vertex is assigned to a layer and each layer is placed on a horizontal line.
Vertices within the same layer are then permuted using the barycenter
heuristic that tries to minimize edge crossings.
Dummy vertices will be added on edges that span more than one layer. The
returned layout therefore contains more rows than the number of nodes in the
original graph; the extra rows correspond to the dummy vertices.
Parameters
layers:

a vector specifying a non-negative integer

layer index for each vertex, or the name
of a numeric vertex attribute that
contains the layer indices. If None, a
layering will be determined automatically.
For undirected graphs, a spanning tree
will be extracted and vertices will be
assigned to layers using a breadth first
search from the node with the largest
degree. For directed graphs, cycles are
broken by reversing the direction of edges
in an approximate feedback arc set using
the heuristic of Eades, Lin and Smyth,
and then using longest path layering to
place the vertices in layers.

weights:

edge weights to be used. Can be a

sequence or iterable or even an edge
attribute name.

hgap:

minimum horizontal gap between vertices

in the same layer.

vgap:

vertical gap between layers. The layer

index will be multiplied by vgap to
obtain the Y coordinate.

maxiter:

maximum number of iterations to take in

the crossing reduction step. Increase this
if you feel that you are getting too many
edge crossings.

return_extended_graph: specifies that the extended graph with

the added dummy vertices should also be
54 When this is True, the result
returned.
will be a tuple containing the layout and
the extended graph. The first |V| nodes
of the extended graph will correspond to

Class Graph

Package igraph

maximum_bipartite_matching(self, types=type, weights=None,

eps=None)
Finds a maximum matching in a bipartite graph.
A maximum matching is a set of edges such that each vertex is incident on at
most one matched edge and the number (or weight) of such edges in the set is
as large as possible.
Parameters
types:

vertex types in a list or the name of a vertex attribute

holding vertex types. Types should be denoted by zeros
and ones (or False and True) for the two sides of the
bipartite graph. If omitted, it defaults to type, which is
the default vertex type attribute for bipartite graphs.

weights: edge weights to be used. Can be a sequence or iterable or

even an edge attribute name.
eps:

a small real number used in equality tests in the weighted

bipartite matching algorithm. Two real numbers are
considered equal in the algorithm if their difference is
smaller than this value. This is required to avoid the
accumulation of numerical errors. If you pass None here,
igraph will try to determine an appropriate value
automatically.

Return Value
an instance of Matching.
write_adjacency(self, f, sep= , eol =\n, *args, **kwds)
Writes the adjacency matrix of the graph to the given file
All the remaining arguments not mentioned here are passed intact to
Graph.get_adjacency.
Parameters
f: the name of the file to be written.
sep: the string that separates the matrix elements in a row
eol: the string that separates the rows of the matrix. Please note
that igraph is able to read back the written adjacency matrix if
and only if this is a single newline character

Class Graph

Package igraph

Read_Adjacency(klass, f, sep=None, comment_char =#, attribute=None,

*args, **kwds)
Constructs a graph based on an adjacency matrix from the given file
Additional positional and keyword arguments not mentioned here are passed
intact to Graph.Adjacency.
Parameters
f:

the name of the file to be read or a file object

the string that separates the matrix elements in a
row. None means an arbitrary sequence of
whitespace characters.

sep:

comment_char: lines starting with this string are treated as

comments.
attribute:

an edge attribute name where the edge weights are

stored in the case of a weighted adjacency matrix. If
None, no weights are stored, values larger than 1 are
considered as edge multiplicities.

Return Value
the created graph
write_dimacs(self, f, source=None, target=None, capacity=capacity)
Writes the graph in DIMACS format to the given file.
Parameters
f:

the name of the file to be written or a Python file handle.

source:

the source vertex ID. If None, igraph will try to infer it

from the source graph attribute.

target:

the target vertex ID. If None, igraph will try to infer it

from the target graph attribute.

capacity: the capacities of the edges in a list or the name of an

edge attribute that holds the capacities. If there is no
such edge attribute, every edge will have a capacity of 1.
Overrides: igraph.GraphBase.write_dimacs

Class Graph

Package igraph

write_graphmlz(self, f, compresslevel =9)

Writes the graph to a zipped GraphML file.
The library uses the gzip compression algorithm, so the resulting file can be
unzipped with regular gzip uncompression (like gunzip or zcat from Unix
command line) or the Python gzip module.
Uses a temporary file to store intermediate GraphML data, so make sure you
have enough free space to store the unzipped GraphML file as well.
Parameters
f:

the name of the file to be written.

compresslevel: the level of compression. 1 is fastest and produces

the least compression, and 9 is slowest and
produces the most compression.
Read_DIMACS(f, directed =False)
Reads a graph from a file conforming to the DIMACS minimum-cost flow file
format.
For the exact definition of the format, see
http://lpsolve.sourceforge.net/5.5/DIMACS.htm.
Restrictions compared to the official description of the format are as follows:
igraphs DIMACS reader requires only three fields in an arc definition,
describing the edges source and target node and its capacity.
Source vertices are identified by s in the FLOW field, target vertices are
identified by t.
Node indices start from 1. Only a single source and target node is allowed.
Parameters
f:

the name of the file or a Python file handle

directed: whether the generated graph should be directed.

Return Value
the generated graph. The indices of the source and target vertices
are attached as graph attributes source and target, the edge
capacities are stored in the capacity edge attribute.
Overrides: igraph.GraphBase.Read_DIMACS

Class Graph

Package igraph

Read_GraphMLz(f, directed =True, index =0)

Reads a graph from a zipped GraphML file.
Parameters
f:
the name of the file
index: if the GraphML file contains multiple graphs, specified the
one that should be loaded. Graph indices start from zero, so
if you want to load the first graph, specify 0 here.
Return Value
the loaded graph object
write_pickle(self, fname=None, version=-1)
Saves the graph in Python pickled format
Parameters
fname:

the name of the file or a stream to save to. If None, saves

the graph to a string and returns the string.

version: pickle protocol version to be used. If -1, uses the highest

protocol available
Return Value
None if the graph was saved successfully to the given file, or a string
if fname was None.
write_picklez(self, fname=None, version=-1)
Saves the graph in Python pickled format, compressed with gzip.
Saving in this format is a bit slower than saving in a Python pickle without
compression, but the final file takes up much less space on the hard drive.
Parameters
fname:

the name of the file or a stream to save to.

version: pickle protocol version to be used. If -1, uses the highest

protocol available
Return Value
None if the graph was saved successfully to the given file.

Class Graph

Package igraph

Read_Pickle(klass, fname=None)
Reads a graph from Python pickled format
Parameters
fname: the name of the file, a stream to read from, or a string
containing the pickled data. The string is assumed to hold
pickled data if it is longer than 40 characters and contains a
substring thats peculiar to pickled versions of an igraph
Graph object.
Return Value
the created graph object.
Read_Picklez(klass, fname, *args, **kwds)
Reads a graph from compressed Python pickled format, uncompressing it
on-the-fly.
Parameters
fname: the name of the file or a stream to read from.
Return Value
the created graph object.

Class Graph

Package igraph

write_svg(self, fname, layout=auto, width=None, height=None,

labels=label, colors=color, shapes=shape, vertex_size=10,
edge_colors=color, font_size=16, *args, **kwds)
Saves the graph as an SVG (Scalable Vector Graphics) file
The file will be Inkscape (http://inkscape.org) compatible. In Inkscape, as
nodes are rearranged, the edges auto-update.
Parameters
fname:

the name of the file

layout:

the layout of the graph. Can be either an explicitly

specified layout (using a list of coordinate pairs) or
the name of a layout algorithm (which should refer to
a method in the Graph object, but without the
layout_ prefix.

width:

the preferred width in pixels (default: 400)

height:

the preferred height in pixels (default: 400)

labels:

the vertex labels. Either it is the name of a vertex

attribute to use, or a list explicitly specifying the
labels. It can also be None.

colors:

the vertex colors. Either it is the name of a vertex

attribute to use, or a list explicitly specifying the
colors. A color can be anything acceptable in an SVG
file.

shapes:

the vertex shapes. Either it is the name of a vertex

attribute to use, or a list explicitly specifying the
shapes as integers. Shape 0 means hidden (nothing is
drawn), shape 1 is a circle, shape 2 is a rectangle and
shape 3 is a rectangle that automatically sizes to the
inner text.

vertex_size: vertex size in pixels

edge_colors: the edge colors. Either it is the name of an edge
attribute to use, or a list explicitly specifying the
colors. A color can be anything acceptable in an SVG
file.
font_size:

font size. If it is a string, it is written into the SVG

file as-is (so you can specify anything which is valid
as the value of the font-size style). If it is a
number, it is interpreted as pixel size and converted
to the proper attribute value accordingly.

Class Graph

Package igraph

Read(klass, f, format=None, *args, **kwds)

Unified reading function for graphs.
This method tries to identify the format of the graph given in the first
parameter and calls the corresponding reader method.
The remaining arguments are passed to the reader method without any
changes.
Parameters
f:
the file containing the graph to be loaded
format: the format of the file (if known in advance). None means
auto-detection. Possible values are: "ncol" (NCOL
format), "lgl" (LGL format), "graphdb" (GraphDB
format), "graphml", "graphmlz" (GraphML and gzipped
GraphML format), "gml" (GML format), "net", "pajek"
(Pajek format), "dimacs" (DIMACS format), "edgelist",
"edges" or "edge" (edge list), "adjacency" (adjacency
matrix), "pickle" (Python pickled format), "picklez"
(gzipped Python pickled format)
Raises
IOError if the file format cant be identified and none was given.

Class Graph

Package igraph

Load(klass, f, format=None, *args, **kwds)

Class Graph

Package igraph

write(self, f, format=None, *args, **kwds)

Unified writing function for graphs.
This method tries to identify the format of the graph given in the first
parameter (based on extension) and calls the corresponding writer method.
The remaining arguments are passed to the writer method without any
changes.
Parameters
f:
the file containing the graph to be saved
format: the format of the file (if one wants to override the format
determined from the filename extension, or the filename
itself is a stream). None means auto-detection. Possible
values are:

"adjacency": adjacency matrix format

"dimacs": DIMACS format
"dot", "graphviz": GraphViz DOT format
"edgelist", "edges" or "edge": numeric edge list
format
"gml": GML format
"graphml" and "graphmlz": standard and gzipped
GraphML format
"gw", "leda", "lgr": LEDA native format
"lgl": LGL format
"ncol": NCOL format
"net", "pajek": Pajek format
"pickle", "picklez": standard and gzipped Python
pickled format
"svg": SVG format

Raises
IOError if the file format cant be identified and none was given.

Class Graph

Package igraph

save(self, f, format=None, *args, **kwds)

"adjacency": adjacency matrix format

Raises
IOError if the file format cant be identified and none was given.

Class Graph

Package igraph

DictList(klass, vertices, edges, directed =False, vertex_name_attr =name,

edge_foreign_keys=(source, target), iterative=False)
Constructs a graph from a list-of-dictionaries representation.
This representation assumes that vertices and edges are encoded in two lists,
each list containing a Python dict for each vertex and each edge, respectively.
A distinguished element of the vertex dicts contain a vertex ID which is used
in the edge dicts to refer to source and target vertices. All the remaining
elements of the dict are considered vertex and edge attributes. Note that the
implementation does not assume that the objects passed to this method are
indeed lists of dicts, but they should be iterable and they should yield objects
that behave as dicts. So, for instance, a database query result is likely to be fit
as long as its iterable and yields dict-like objects with every iteration.
Parameters
vertices:

the data source for the vertices or None if

there are no special attributes assigned to
vertices and we should simply use the edge list
of dicts to infer vertex names.

edges:

the data source for the edges.

directed:

whether the constructed graph will be directed

vertex_name_attr: the name of the distinguished key in the dicts

in the vertex data source that contains the
vertex names. Ignored if vertices is None.
edge_foreign_keys: the name of the attributes in the dicts in the
edge data source that contain the source and
target vertex names.
iterative:

whether to add the edges to the graph one by

one, iteratively, or to build a large edge list
first and use that to construct the graph. The
latter approach is faster but it may not be
suitable if your dataset is large. The default is
to add the edges in a batch from an edge list.

Return Value
the graph that was constructed

Class Graph

Package igraph

TupleList(klass, edges, directed =False, vertex_name_attr =name,

edge_attrs=None, weights=False)
Constructs a graph from a list-of-tuples representation.
This representation assumes that the edges of the graph are encoded in a list
of tuples (or lists). Each item in the list must have at least two elements,
which specify the source and the target vertices of the edge. The remaining
elements (if any) specify the edge attributes of that edge, where the names of
the edge attributes originate from the edge_attrs list. The names of the
vertices will be stored in the vertex attribute given by vertex_name_attr.
The default parameters of this function are suitable for creating unweighted
graphs from lists where each item contains the source vertex and the target
vertex. If you have a weighted graph, you can use items where the third item
contains the weight of the edge by setting edge_attrs to "weight" or
["weight"]. If you have even more edge attributes, add them to the end of
each item in the edges list and also specify the corresponding edge attribute
names in edge_attrs as a list.
Parameters
edges:

directed:

the data source for the edges. This must be a

list where each item is a tuple (or list)
containing at least two items: the name of the
source and the target vertex. Note that names
will be assigned to the name vertex attribute
(or another vertex attribute if
vertex_name_attr is specified), even if all the
vertex names in the list are in fact numbers.
whether the constructed graph will be directed

vertex_name_attr: the name of the vertex attribute that will

contain the vertex names.
edge_attrs:

the names of the edge attributes that are filled

with the extra items in the edge list (starting
from index 2, since the first two items are the
source and target vertices). None means that
only the source and target vertices will be
extracted from each item. If you pass a string
here, it will be wrapped in a list for
convenience.

weights:

alternative way to specify that the graph is

weighted. If you set weights to true and
edge_attrs is not given, it will be assumed
that edge_attrs is ["weight"] and igraph will
parse the third element from each item into an
edge weight. If you set weights to a string, it
66 that edge_attrs contains that
will be assumed
string only, and igraph will store the edge
weights in that attribute.

Return Value

Class Graph

Package igraph

Formula(Graph, formula=None, attr ="name", simplify=True)

Generates a graph from a graph formula
A graph formula is a simple string representation of a graph. It is very handy
for creating small graphs quickly. The string consists of vertex names
separated by edge operators. An edge operator is a sequence of dashes (-) that
may or may not start with an arrowhead (< at the beginning of the sequence
or > at the end of the sequence). The edge operators can be arbitrarily long,
i.e., you may use as many dashes to draw them as you like. This makes a total
of four different edge operators:
- makes an undirected edge
< makes a directed edge pointing from the vertex on the right hand side
of the operator to the vertex on the left hand side
> is the opposite of <
<-> creates a mutual directed edge pair between the two vertices
If you only use the undirected edge operator (-), the graph will be
undirected. Otherwise it will be directed. Vertex names used in the formula
will be assigned to the name vertex attribute of the graph.
Some simple examples:
igraph import Graph
print Graph.Formula()

>>> from
>>>

# empty graph

IGRAPH UN-- 0 0 -+ attr: name (v)

>>>
>>>

g = Graph.Formula("A-B")
g.vs["name"]

# undirected graph

[A, B]
>>> print

IGRAPH UN-- 2 1 -+ attr: name (v)

+ edges (vertex names):
A--B
>>>

g.get_edgelist()

[(0, 1)]
>>>
>>>

g2 = Graph.Formula("A-----------B")
g2.isomorphic(g)

True
>>>
>>>

g = Graph.Formula("A
g.vs["name"]

--->

B") # directed graph

[A, B]
>>> print

IGRAPH DN-- 2 1 -+ attr: name (v)

+ edges (vertex names):

A->B

If you have may disconnected componnets, you can separate them with
commas. You can also specify isolated vertices:

Class Graph

Package igraph

Bipartite(types, edges, directed =False)

Creates a bipartite graph with the given vertex types and edges. This is
similar to the default constructor of the graph, the only difference is that it
checks whether all the edges go between the two vertex classes and it assigns
the type vector to a type attribute afterwards.
Examples:
>>>
>>>

g = Graph.Bipartite([0, 1, 0, 1], [(0, 1), (2, 3), (0, 3)])

g.is_bipartite()

True
>>>

g.vs["type"]

[False, True, False, True]

Parameters
types:

edges:

the vertex types as a boolean list. Anything that

evaluates to False will denote a vertex of the first kind,
anything that evaluates to True will denote a vertex of
the second kind.
the edges as a list of tuples.

directed: whether to create a directed graph. Bipartite networks

are usually undirected, so the default is False
Return Value
the graph with a binary vertex attribute named "type" that stores
the vertex classes.

Class Graph

Package igraph

Full_Bipartite(n1, n2, directed =False, mode=ALL)

Generates a full bipartite graph (directed or undirected, with or without
loops).
>>>
>>>

g = Graph.Full_Bipartite(2, 3)
g.is_bipartite()

True
>>>

g.vs["type"]

[False, False, True, True, True]

Parameters
n1:
n2:

the number of vertices of the first kind.

the number of vertices of the second kind.

directed: whether tp generate a directed graph.

mode:

if OUT, then all vertices of the first kind are connected to

the others; IN specifies the opposite direction, ALL
creates mutual edges. Ignored for undirected graphs.

Return Value
the graph with a binary vertex attribute named "type" that stores
the vertex classes.

Class Graph

Package igraph

Random_Bipartite(klass, *args, **kwds)

Generates a random bipartite graph with the given number of vertices and
edges (if m is given), or with the given number of vertices and the given
connection probability (if p is given).
If m is given but p is not, the generated graph will have n1 vertices of type 1,
n2 vertices of type 2 and m randomly selected edges between them. If p is
given but m is not, the generated graph will have n1 vertices of type 1 and n2
vertices of type 2, and each edge will exist between them with probability p.
Parameters
n1:

the number of vertices of type 1.

n2:

the number of vertices of type 2.

the probability of edges. If given, m must be missing.

the number of edges. If given, p must be missing.

directed: whether to generate a directed graph.

neimode: if the graph is directed, specifies how the edges will be
generated. If it is "all", edges will be generated in both
directions (from type 1 to type 2 and vice versa)
independently. If it is "out" edges will always point from
type 1 to type 2. If it is "in", edges will always point
from type 2 to type 1. This argument is ignored for
undirected graphs.
GRG(n, radius, torus=False, return_coordinates=False)
Generates a random geometric graph.
The algorithm drops the vertices randomly on the 2D unit square and
connects them if they are closer to each other than the given radius. The
coordinates of the vertices are stored in the vertex attributes x and y.
Parameters
n:
The number of vertices in the graph
radius: The given radius
torus: This should be True if we want to use a torus instead of a
square.

Class Graph

Package igraph

Incidence(matrix, directed =False, mode=ALL, multiple=False)

Creates a bipartite graph from an incidence matrix.
Example:
>>>

g = Graph.Incidence([[0, 1, 1], [1, 1, 0]])

Parameters
matrix:

the incidence matrix.

directed: whether to create a directed graph.

mode:

defines the direction of edges in the graph. If OUT, then

edges go from vertices of the first kind (corresponding to
rows of the matrix) to vertices of the second kind (the
columns of the matrix). If IN, the opposite direction is
used. ALL creates mutual edges. Ignored for undirected
graphs.

multiple: defines what to do with non-zero entries in the matrix. If

False, non-zero entries will create an edge no matter
what the value is. If True, non-zero entries are rounded
up to the nearest integer and this will be the number of
multiple edges created.
Return Value
the graph with a binary vertex attribute named "type" that stores
the vertex classes.

Class Graph

Package igraph

bipartite_projection(self, types=type, multiplicity=True, probe1 =-1,

which=both)
Projects a bipartite graph into two one-mode graphs. Edge directions are
ignored while projecting.
Examples:
>>>
>>>
>>>

g = Graph.Full_Bipartite(10, 5)
g1, g2 = g.bipartite_projection()
g1.isomorphic(Graph.Full(10))

True
>>>

g2.isomorphic(Graph.Full(5))

True

Parameters
types:

an igraph vector containing the vertex types, or an

attribute name. Anything that evalulates to False
corresponds to vertices of the first kind, everything
else to the second kind.

multiplicity: if True, then igraph keeps the multiplicity of the

edges in the projection in an edge attribute called
"weight". E.g., if there is an A-C-B and an A-D-B
triplet in the bipartite graph and there is no other X
(apart from X=B and X=D) for which an A-X-B
triplet would exist in the bipartite graph, the
multiplicity of the A-B edge in the projection will
be 2.
probe1:

this argument can be used to specify the order of

the projections in the resulting list. If given and
non-negative, then it is considered as a vertex ID;
the projection containing the vertex will be the first
one in the result.

which:

this argument can be used to specify which of the

two projections should be returned if only one of
them is needed. Passing 0 here means that only the
first projection is returned, while 1 means that only
the second projection is returned. (Note that we use
0 and 1 because Python indexing is zero-based).
False is equivalent to 0 and True is equivalent to 1.
Any other value means that both projections will be
returned in a tuple.

Return Value
a tuple containing the two projected one-mode graphs if which is not
1 or 2, or the projected one-mode graph specified by the which
argument if its value is 0, 1, False or True.
72

Overrides: igraph.GraphBase.bipartite_projection

Class Graph

Package igraph

bipartite_projection_size(types="type")
Calculates the number of vertices and edges in the bipartite projections of this
graph according to the specified vertex types. This is useful if you have a
bipartite graph and you want to estimate the amount of memory you would
need to calculate the projections themselves.
Parameters
types: an igraph vector containing the vertex types, or an attribute
name. Anything that evalulates to False corresponds to
vertices of the first kind, everything else to the second kind.
Return Value
a 4-tuple containing the number of vertices and edges in the first
projection, followed by the number of vertices and edges in the
second projection.
Overrides: igraph.GraphBase.bipartite_projection_size
get_incidence(self, types="type")
Returns the incidence matrix of a bipartite graph. The incidence matrix is an
n times m matrix, where n and m are the number of vertices in the two vertex
classes.
Parameters
types: an igraph vector containing the vertex types, or an attribute
name. Anything that evalulates to False corresponds to
vertices of the first kind, everything else to the second kind.
Return Value
the incidence matrix and two lists in a triplet. The first list defines
the mapping between row indices of the matrix and the original
vertex IDs. The second list is the same for the column indices.
Overrides: igraph.GraphBase.get_incidence
__iadd__(self, other )
In-place addition (disjoint union).
See Also: __add__

Class Graph

Package igraph

__add__(self, other )
Copies the graph and extends the copy depending on the type of the other
object given.
Parameters
other: if it is an integer, the copy is extended by the given number
of vertices. If it is a string, the copy is extended by a single
vertex whose name attribute will be equal to the given string.
If it is a tuple with two elements, the copy is extended by a
single edge. If it is a list of tuples, the copy is extended by
multiple edges. If it is a Graph, a disjoint union is performed.
__isub__(self, other )
In-place subtraction (difference).
See Also: __sub__
__sub__(self, other )
Removes the given object(s) from the graph
Parameters
other: if it is an integer, removes the vertex with the given ID from
the graph (note that the remaining vertices will get
re-indexed!). If it is a tuple, removes the given edge. If it is
a graph, takes the difference of the two graphs. Accepts lists
of integers or lists of tuples as well, but they cant be mixed!
Also accepts Edge and EdgeSeq objects.
__mul__(self, other )
Copies exact replicas of the original graph an arbitrary number of times.
Parameters
other: if it is an integer, multiplies the graph by creating the given
number of identical copies and taking the disjoint union of
them.
__nonzero__(self )
Returns True if the graph has at least one vertex, False otherwise.

Class Graph

Package igraph

__coerce__(self, other )
Coercion rules.
This method is needed to allow the graph to react to additions with lists,
tuples, integers, strings, vertices, edges and so on.
__reduce__(self )
Support for pickling.
Overrides: object.__reduce__

Class Graph

Package igraph

plot(self, context, bbox, palette, *args, **kwds)

Plots the graph to the given Cairo context in the given bounding box
The visual style of vertices and edges can be modified at three places in the
following order of precedence (lower indices override higher indices):
1. Keyword arguments of this function (or of plot() which is passed intact
to Graph.__plot__().
2. Vertex or edge attributes, specified later in the list of keyword arguments.
3. igraph-wide plotting defaults (see igraph.config.Configuration)
4. Built-in defaults.
E.g., if the vertex_size keyword attribute is not present, but there exists a
vertex attribute named size, the sizes of the vertices will be specified by that
attribute.
Besides the usual self-explanatory plotting parameters (context, bbox,
palette), it accepts the following keyword arguments:
autocurve: whether to use curves instead of straight lines for multiple
edges on the graph plot. This argument may be True or False; when
omitted, True is assumed for graphs with less than 10.000 edges and
False otherwise.
drawer_factory: a subclass of AbstractCairoGraphDrawer which will
be used to draw the graph. You may also provide a function here which
takes two arguments: the Cairo context to draw on and a bounding box
(an instance of BoundingBox). If this keyword argument is missing,
igraph will use the default graph drawer which should be suitable for
most purposes. It is safe to omit this keyword argument unless you need
to use a specific graph drawer.
keep_aspect_ratio: whether to keep the aspect ratio of the layout that
igraph calculates to place the nodes. True means that the layout will be
scaled proportionally to fit into the bounding box where the graph is to
be drawn but the aspect ratio will be kept the same (potentially leaving
empty space next to, below or above the graph). False means that the
layout will be scaled independently along the X and Y axis in order to fill
the entire bounding box. The default is False.
layout: the layout to be used. If not an instance of Layout, it will be
passed to Graph.layout to calculate the layout. Note that if you want a
deterministic layout that does not change with every plot, you must
either use a deterministic layout function (like Graph.layout_circle) or
calculate the layout in advance and pass a Layout object here.
margin: the top, right, bottom, left margins as a 4-tuple. If it has less
than 4 elements or is a single float, the elements will be re-used until the
length is at least 4.
mark_groups: whether to highlight76some of the vertex groups by colored
polygons. This argument can be one of the following:
False: no groups will be highlighted
A dict mapping tuples of vertex indices to color names. The given

Class Graph

Package igraph

__str__(self )
Returns a string representation of the graph.
Behind the scenes, this method constructs a GraphSummary instance and
invokes its __str__ method with a verbosity of 1 and attribute printing
turned off.
See the documentation of GraphSummary for more details about the output.
Overrides: object.__str__
summary(self, verbosity=0, width=None, *args, **kwds)
Returns the summary of the graph.
The output of this method is similar to the output of the __str__ method. If
verbosity is zero, only the header line is returned (see __str__ for more
details), otherwise the header line and the edge list is printed.
Behind the scenes, this method constructs a GraphSummary object and invokes
its __str__ method.
Parameters
verbosity: if zero, only the header line is returned (see __str__ for
more details), otherwise the header line and the full
edge list is printed.
width:

the number of characters to use in one line. If None, no

limit will be enforced on the line lengths.

Return Value
the summary of the graph.
layout_fruchterman_reingold_3d(*args, **kwds)
Alias for layout_fruchterman_reingold() with dim=3.
See Also: Graph.layout_fruchterman_reingold()
layout_kamada_kawai_3d(*args, **kwds)
Alias for layout_kamada_kawai() with dim=3.
See Also: Graph.layout_kamada_kawai()
layout_random_3d(*args, **kwds)
Alias for layout_random() with dim=3.
See Also: Graph.layout_random()
77

Class Graph

Package igraph

layout_grid_3d(*args, **kwds)
Alias for layout_grid() with dim=3.
See Also: Graph.layout_grid()
layout_sphere(*args, **kwds)
Alias for layout_circle() with dim=3.
See Also: Graph.layout_circle()
layout_bipartite(types="type", hgap=1, vgap=1, maxiter =100)
Place the vertices of a bipartite graph in two layers.
The layout is created by placing the vertices in two rows, according to their
types. The positions of the vertices within the rows are then optimized to
minimize the number of edge crossings using the heuristic used by the
Sugiyama layout algorithm.
Parameters
types:

an igraph vector containing the vertex types, or an

attribute name. Anything that evalulates to False
corresponds to vertices of the first kind, everything else to
the second kind.

hgap:

minimum horizontal gap between vertices in the same

layer.

vgap:

vertical gap between the two layers.

maxiter: maximum number of iterations to take in the crossing

reduction step. Increase this if you feel that you are
getting too many edge crossings.
Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_bipartite

Class Graph

Package igraph

layout_circle(dim=2)
Places the vertices of the graph uniformly on a circle or a sphere.
Parameters
dim: the desired number of dimensions for the layout. dim=2 means
a 2D layout, dim=3 means a 3D layout.
Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_circle

Class Graph

Package igraph

layout_drl(weights=None, fixed =None, seed =None, options=None, dim=2)

Places the vertices on a 2D plane or in the 3D space ccording to the DrL
layout algorithm.
This is an algorithm suitable for quite large graphs, but it can be surprisingly
slow for small ones (where the simpler force-based layouts like
layout_kamada_kawai() or layout_fruchterman_reingold() are more
useful.
Parameters
weights: edge weights to be used. Can be a sequence or iterable or
even an edge attribute name.
seed:

if None, uses a random starting layout for the algorithm.

If a matrix (list of lists), uses the given matrix as the
starting position.

fixed:

if a seed is given, you can specify some vertices to be kept

fixed at their original position in the seed by passing an
appropriate list here. The list must have exactly as many
items as the number of vertices in the graph. Items of the
list that evaluate to True denote vertices that will not be
moved.

options: if you give a string argument here, you can select from five
default preset parameterisations: default, coarsen for a
coarser layout, coarsest for an even coarser layout,
refine for refining an existing layout and final for
finalizing a layout. If you supply an object that is not a
string, the DrL layout parameters are retrieved from the
respective keys of the object (so it should be a dict or
something else that supports the mapping protocol). The
following keys can be used:
edge_cut: edge cutting is done in the late stages of
the algorithm in order to achieve less dense layouts.
Edges are cut if there is a lot of stress on them (a large
value in the objective function sum). The edge cutting
parameter is a value between 0 and 1 with 0
representing no edge cutting and 1 representing
maximal edge cutting.
init_iterations: number of iterations in the
initialization phase
init_temperature: start temperature during
initialization
init_attraction: attraction during initialization
init_damping_mult: damping multiplier during
initialization
80
liquid_iterations, liquid_temperature,
liquid_attraction, liquid_damping_mult: same
parameters for the liquid phase
expansion_iterations, expansion_temperature,

Class Graph

Package igraph

layout_fruchterman_reingold(weights=None, maxiter =500,

maxdelta=None, area=None, coolexp=1.5, repulserad =None, seed =None,
minx =None, maxx =None, miny=None, maxy=None, minz =None, maxz =None,
dim=2)
Places the vertices on a 2D plane or in the 3D space according to the
Fruchterman-Reingold algorithm.
This is a force directed layout, see Fruchterman, T. M. J. and Reingold, E. M.:
Graph Drawing by Force-directed Placement. Software Practice and
Experience, 21/11, 11291164, 1991
Parameters
weights:

edge weights to be used. Can be a sequence or iterable

or even an edge attribute name.

maxiter:

the number of iterations to perform. The default is

500.

maxdelta:

the maximum distance to move a vertex in an

iteration. The default is the number of vertices.

area:

the area of the square on which the vertices will be

placed. The default is the square of the number of
vertices.

coolexp:

the cooling exponent of the simulated annealing. The

default is 1.5.

repulserad: determines the radius at which vertex-vertex repulsion

cancels out attraction of adjacent vertices. The default
is the number of vertices^3.
minx:

if not None, it must be a vector with exactly as many

elements as there are vertices in the graph. Each
element is a minimum constraint on the X value of the
vertex in the layout.

maxx:

similar to minx, but with maximum constraints

miny:

similar to minx, but with the Y coordinates

maxy:

similar to maxx, but with the Y coordinates

minz:

similar to minx, but with the Z coordinates. Use only

for 3D layouts (dim=3).

maxz:

similar to maxx, but with the Z coordinates. Use only

for 3D layouts (dim=3).

seed:

if None, uses a random starting layout for the

algorithm. If a matrix (list of lists), uses the given
matrix as the starting position.

dim:

the desired number of dimensions for the layout.

dim=2 means a 2D layout,
dim=3 means a 3D layout.
81

Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_fruchterman_reingold

Class Graph

Package igraph

layout_graphopt(niter =500, node_charge=0.001, node_mass=30,

spring_length=0, spring_constant=1, max_sa_movement=5, seed =None)
This is a port of the graphopt layout algorithm by Michael Schmuhl. graphopt
version 0.4.1 was rewritten in C and the support for layers was removed.
graphopt uses physical analogies for defining attracting and repelling forces
among the vertices and then the physical system is simulated until it reaches
an equilibrium or the maximal number of iterations is reached.
See http://www.schmuhl.org/graphopt/ for the original graphopt.
Parameters
niter:

the number of iterations to perform. Should be a

couple of hundred in general.

node_charge:

the charge of the vertices, used to calculate

electric repulsion.

node_mass:

the mass of the vertices, used for the spring

forces

spring_length:

the length of the springs

spring_constant: the spring constant

max_sa_movement: the maximum amount of movement allowed in a
single step along a single axis.
seed:

a matrix containing a seed layout from which

the algorithm will be started. If None, a random
layout will be used.

Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_graphopt

Class Graph

Package igraph

layout_grid(width=0, height=0, dim=2)

Places the vertices of a graph in a 2D or 3D grid.
Parameters
width: the number of vertices in a single row of the layout. Zero or
negative numbers mean that the width should be
determined automatically.
height: the number of vertices in a single column of the layout.
Zero or negative numbers mean that the height should be
determined automatically. It must not be given if the
number of dimensions is 2.
dim:

the desired number of dimensions for the layout. dim=2

means a 2D layout, dim=3 means a 3D layout.

Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_grid

Class Graph

Package igraph

layout_grid_fruchterman_reingold(maxiter =500, maxdelta=None,

area=None, coolexp=0.99, repulserad =maxiter*maxdelta, cellsize=None,
seed =None)
Places the vertices on a 2D plane according to the Fruchterman-Reingold grid
algorithm.
This is a modified version of a force directed layout, see Fruchterman, T. M. J.
and Reingold, E. M.: Graph Drawing by Force-directed Placement. Software
Practice and Experience, 21/11, 11291164, 1991. The algorithm partitions
the 2D space to a grid and vertex repulsion is then calculated only for vertices
nearby.
Parameters
maxiter:

the number of iterations to perform.

maxdelta:

the maximum distance to move a vertex in an

iteration. None means the number of vertices.

area:

the area of the square on which the vertices will be

placed. None means the square of maxdelta.

coolexp:

the cooling exponent of the simulated annealing.

repulserad: determines the radius at which vertex-vertex repulsion

cancels out attraction of adjacent vertices. None means
maxiter*maxdelta.
cellsize:

the size of the grid cells. When calculating the

repulsion forces, only vertices in the same or
neighboring grid cells are taken into account. Defaults
to the fourth root of area.

seed:

if None, uses a random starting layout for the

algorithm. If a matrix (list of lists), uses the given
matrix as the starting position.

Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_grid_fruchterman_reingold

Class Graph

Package igraph

layout_kamada_kawai(maxiter =1000, sigma=None, initemp=10,

coolexp=0.99, kkconst=None, seed =None, minx =None, maxx =None,
miny=None, maxy=None, minz =None, maxz =None, dim=2)
Places the vertices on a plane according to the Kamada-Kawai algorithm.
This is a force directed layout, see Kamada, T. and Kawai, S.: An Algorithm
for Drawing General Undirected Graphs. Information Processing Letters,
31/1, 715, 1989.
Parameters
maxiter: the number of iterations to perform.
sigma:

the standard base deviation of the position change

proposals. None means the number of vertices / 4

initemp: initial temperature of the simulated annealing.

coolexp: cooling exponent of the simulated annealing.
kkconst: the Kamada-Kawai vertex attraction constant. None
means the square of the number of vertices.
minx:

if not None, it must be a vector with exactly as many

elements as there are vertices in the graph. Each element
is a minimum constraint on the X value of the vertex in
the layout.

maxx:

similar to minx, but with maximum constraints

miny:

similar to minx, but with the Y coordinates

maxy:

similar to maxx, but with the Y coordinates

minz:

similar to minx, but with the Z coordinates. Use only for

3D layouts (dim=3).

maxz:

similar to maxx, but with the Z coordinates. Use only for

3D layouts (dim=3).

seed:

if None, uses a random starting layout for the algorithm.

If a matrix (list of lists), uses the given matrix as the
starting position.

dim:

the desired number of dimensions for the layout. dim=2

means a 2D layout, dim=3 means a 3D layout.

Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_kamada_kawai

Class Graph

Package igraph

layout_lgl(maxiter =150, maxdelta=-1, area=-1, coolexp=1.5,

repulserad =-1, cellsize=-1, root=None)
Places the vertices on a 2D plane according to the Large Graph Layout.
Parameters
maxiter:

the number of iterations to perform.

maxdelta:

the maximum distance to move a vertex in an

iteration. If negative, defaults to the number of
vertices.

area:

the area of the square on which the vertices will be

placed. If negative, defaults to the number of vertices
squared.

coolexp:

the cooling exponent of the simulated annealing.

repulserad: determines the radius at which vertex-vertex repulsion

cancels out attraction of adjacent vertices. If negative,
defaults to area times the number of vertices.
cellsize:

the size of the grid cells. When calculating the

repulsion forces, only vertices in the same or
neighboring grid cells are taken into account. Defaults
to the fourth root of area.

root:

the root vertex, this is placed first, its neighbors in the

first iteration, second neighbors in the second, etc.
None means that a random vertex will be chosen.

Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_lgl

Class Graph

Package igraph

layout_mds(dist=None, dim=2, arpack_options=None)

Places the vertices in an Euclidean space with the given number of dimensions
using multidimensional scaling.
This layout requires a distance matrix, where the intersection of row i and
column j specifies the desired distance between vertex i and vertex j. The
algorithm will try to place the vertices in a way that approximates the
distance relations prescribed in the distance matrix. igraph uses the classical
multidimensional scaling by Torgerson (see reference below).
For unconnected graphs, the method will decompose the graph into weakly
connected components and then lay out the components individually using the
appropriate parts of the distance matrix.
Parameters
dist:

dim:

the distance matrix. It must be symmetric and

the symmetry is not checked results are
unspecified when a non-symmetric distance
matrix is used. If this parameter is None, the
shortest path lengths will be used as distances.
Directed graphs are treated as undirected when
calculating the shortest path lengths to ensure
symmetry.
the number of dimensions. For 2D layouts, supply
2 here; for 3D layouts, supply 3.

arpack_options: an ARPACKOptions object used to fine-tune the

ARPACK eigenvector calculation. If omitted, the
module-level variable called arpack_options is
used.
Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_mds
Reference: Cox & Cox: Multidimensional Scaling (1994), Chapman and Hall,
London.

Class Graph

Package igraph

layout_random(dim=2)
Places the vertices of the graph randomly.
Parameters
dim: the desired number of dimensions for the layout. dim=2 means
a 2D layout, dim=3 means a 3D layout.
Return Value
the coordinate pairs in a list.
Overrides: igraph.GraphBase.layout_random
layout_reingold_tilford(mode="out", root=None, rootlevel =None)
Places the vertices on a 2D plane according to the Reingold-Tilford layout
algorithm.
This is a tree layout. If the given graph is not a tree, a breadth-first search is
executed first to obtain a possible spanning tree.
Parameters
mode:

root:

specifies which edges to consider when builing the tree.

If it is OUT then only the outgoing, if it is IN then only
the incoming edges of a parent are considered. If it is
ALL then all edges are used (this was the behaviour in
igraph 0.5 and before). This parameter also influences
how the root vertices are calculated if they are not
given. See the root parameter.
the index of the root vertex or root vertices. if this is a
non-empty vector then the supplied vertex IDs are used
as the roots of the trees (or a single tree if the graph is
connected. If this is None or an empty list, the root
vertices are automatically calculated based on
topological sorting, performed with the opposite of the
mode argument.

rootlevel: this argument is useful when drawing forests which are

not trees. It specifies the level of the root vertices for
every tree in the forest.
Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_reingold_tilford
See Also: layout_reingold_tilford_circular
Reference: EM Reingold, JS Tilford: Tidier Drawings of Trees. IEEE
Transactions on Software Engineering 7:22, 223-228, 1981.

Class Graph

Package igraph

layout_reingold_tilford_circular(mode="out", root=None,
rootlevel =None)
Circular Reingold-Tilford layout for trees.
This layout is similar to the Reingold-Tilford layout, but the vertices are
placed in a circular way, with the root vertex in the center.
See layout_reingold_tilford for the explanation of the parameters.
Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_reingold_tilford_circular
See Also: layout_reingold_tilford
Reference: EM Reingold, JS Tilford: Tidier Drawings of Trees. IEEE
Transactions on Software Engineering 7:22, 223-228, 1981.
layout_star(center =0, order =None)
Calculates a star-like layout for the graph.
Parameters
center: the ID of the vertex to put in the center
order: a numeric vector giving the order of the vertices (including
the center vertex!). If it is None, the vertices will be placed
in increasing vertex ID order.
Return Value
the calculated layout.
Overrides: igraph.GraphBase.layout_star
Inherited from igraph.GraphBase(Section 1.11)
Adjacency(), Asymmetric_Preference(), Atlas(), Barabasi(), De_Bruijn(), Degree_Sequence(), Erdos_Renyi(), Establishment(), Famous(), Forest_Fire(), Full(),
Full_Citation(), Growing_Random(), Isoclass(), K_Regular(), Kautz(), LCF(),
Lattice(), Preference(), Read_DL(), Read_Edgelist(), Read_GML(), Read_GraphDB(),
Read_GraphML(), Read_Lgl(), Read_Ncol(), Read_Pajek(), Recent_Degree(),
Ring(), SBM(), Star(), Static_Fitness(), Static_Power_Law(), Tree(), Watts_Strogatz(),
Weighted_Adjacency(), __and__(), __delitem__(), __getitem__(), __invert__(), __new__(), __or__(), __rand__(), __ror__(), __setitem__(),
all_minimal_st_separators(), are_connected(), articulation_points(), assortativity(), assortativity_degree(), assortativity_nominal(), attributes(), authority_score(),
average_path_length(), betweenness(), bfs(), bfsiter(), bibcoupling(), canonical_permutation(),
clique_number(), cliques(), closeness(), cocitation(), complementer(), compose(),
constraint(), contract_vertices(), convergence_degree(), convergence_field_size(),
89

Class Graph

Package igraph

copy(), coreness(), count_isomorphisms_vf2(), count_multiple(), count_subisomorphisms_vf2(),

decompose(), degree(), delete_vertices(), density(), diameter(), difference(), disjoint_union(), diversity(), eccentricity(), ecount(), edge_attributes(), edge_betweenness(),
edge_connectivity(), eigenvector_centrality(), farthest_points(), feedback_arc_set(),
get_all_shortest_paths(), get_diameter(), get_edgelist(), get_eid(), get_eids(),
get_isomorphisms_vf2(), get_shortest_paths(), get_subisomorphisms_lad(), get_subisomorphisms_
girth(), has_multiple(), hub_score(), incident(), independence_number(), independent_vertex_sets(), induced_subgraph(), intersection(), is_bipartite(), is_connected(),
is_dag(), is_directed(), is_loop(), is_minimal_separator(), is_multiple(), is_mutual(),
is_separator(), is_simple(), isoclass(), isomorphic(), isomorphic_bliss(), isomorphic_vf2(), knn(), laplacian(), largest_cliques(), largest_independent_vertex_sets(),
linegraph(), maxdegree(), maxflow_value(), maximal_cliques(), maximal_independent_vertex_sets(
mincut_value(), minimum_size_separators(), motifs_randesu(), motifs_randesu_estimate(),
motifs_randesu_no(), neighborhood(), neighborhood_size(), neighbors(), permute_vertices(),
personalized_pagerank(), predecessors(), radius(), reciprocity(), rewire(), rewire_edges(),
shortest_paths(), similarity_dice(), similarity_inverse_log_weighted(), similarity_jaccard(), simplify(), strength(), subcomponent(), subgraph_edges(), subisomorphic_lad(), subisomorphic_vf2(), successors(), to_directed(), to_undirected(),
topological_sorting(), transitivity_local_undirected(), transitivity_undirected(),
unfold_tree(), union(), vcount(), vertex_attributes(), vertex_connectivity(), write_dot(),
write_edgelist(), write_gml(), write_graphml(), write_leda(), write_lgl(), write_ncol(),
write_pajek()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __reduce_ex__(),
__repr__(), __setattr__(), __sizeof__(), __subclasshook__()
1.5.2

Properties

Name
vs
es
Inherited from object
__class__

Description
The vertex sequence of the graph
The edge sequence of the graph

Class VertexSeq

1.6

Package igraph

Class VertexSeq

object
igraph.drawing.graph.VertexSeq
igraph.VertexSeq
Class representing a sequence of vertices in the graph.
This class is most easily accessed by the vs field of the Graph object, which returns an
ordered sequence of all vertices in the graph. The vertex sequence can be refined by invoking
the VertexSeq.select() method. VertexSeq.select() can also be accessed by simply
calling the VertexSeq object.
An alternative way to create a vertex sequence referring to a given graph is to use the
constructor directly:
>>>
>>>
>>>

g = Graph.Full(3)
vs = VertexSeq(g)
restricted_vs = VertexSeq(g, [0, 1])

The individual vertices can be accessed by indexing the vertex sequence object. It can be
used as an iterable as well, or even in a list comprehension:
>>>
>>>
...

g=Graph.Full(3)
for v in g.vs:
v["value"] = v.index ** 2

...
>>>

[v["value"] ** 0.5

for

g.vs]

[0.0, 1.0, 2.0]

The vertex set can also be used as a dictionary where the keys are the attribute names.
The values corresponding to the keys are the values of the given attribute for every vertex
selected by the sequence.
>>>

g=Graph.Full(3)
idx, v in enumerate(g.vs):
v["weight"] = idx*(idx+1)

>>> for
...
...
>>>

g.vs["weight"]

[0, 2, 6]
>>>
>>>

g.vs.select(1,2)["weight"] = [10, 20]

g.vs["weight"]

[0, 10, 20]

If you specify a sequence that is shorter than the number of vertices in the VertexSeq, the

Class VertexSeq

Package igraph

sequence is reused:
>>>
>>>
>>>

g = Graph.Tree(7, 2)
g.vs["color"] = ["red",
g.vs["color"]

"green"]

[red, green, red, green, red, green, red]

You can even pass a single string or integer, it will be considered as a sequence of length 1:
>>>
>>>

g.vs["color"] =
g.vs["color"]

"red"

[red, red, red, red, red, red, red]

Some methods of the vertex sequences are simply proxy methods to the corresponding methods in the Graph object. One such example is VertexSeq.degree():
>>>
>>>

g=Graph.Tree(7, 2)
g.vs.degree()

[2, 3, 3, 1, 1, 1, 1]
>>>

g.vs.degree() == g.degree()

True

1.6.1

Methods

attributes(self )
Returns the list of all the vertex attributes in the graph associated to this
vertex sequence.
find(self, *args, **kwds)
Returns the first vertex of the vertex sequence that matches some criteria.
The selection criteria are equal to the ones allowed by VertexSeq.select. See
VertexSeq.select for more details.
For instance, to find the first vertex with name foo in graph g:
>>>

g.vs.find(name="foo")

#doctest:+SKIP

To find an arbitrary isolated vertex:

>>>

g.vs.find(_degree=0)

#doctest:+SKIP

Return Value
Vertex
Overrides: igraph.drawing.graph.VertexSeq.find

Class VertexSeq

Package igraph

select(self, *args, **kwds)

Selects a subset of the vertex sequence based on some criteria
The selection criteria can be specified by the positional and the keyword
arguments. Positional arguments are always processed before keyword
arguments.
If the first positional argument is None, an empty sequence is returned.
If the first positional argument is a callable object, the object will be
called for every vertex in the sequence. If it returns True, the vertex will
be included, otherwise it will be excluded.
If the first positional argument is an iterable, it must return integers and
they will be considered as indices of the current vertex set (NOT the
whole vertex set of the graph the difference matters when one filters a
vertex set that has already been filtered by a previous invocation of
VertexSeq.select(). In this case, the indices do not refer directly to the
vertices of the graph but to the elements of the filtered vertex sequence.
If the first positional argument is an integer, all remaining arguments are
expected to be integers. They are considered as indices of the current
vertex set again.
Keyword arguments can be used to filter the vertices based on their attributes.
The name of the keyword specifies the name of the attribute and the filtering
operator, they should be concatenated by an underscore (_) character.
Attribute names can also contain underscores, but operator names dont, so
the operator is always the largest trailing substring of the keyword name that
does not contain an underscore. Possible operators are:

eq: equal to
ne: not equal to
lt: less than
gt: greater than
le: less than or equal to
ge: greater than or equal to
in: checks if the value of an attribute is in a given list
notin: checks if the value of an attribute is not in a given list

For instance, if you want to filter vertices with a numeric age property larger
than 200, you have to write:
>>>

g.vs.select(age_gt=200)

#doctest: +SKIP

Similarly, to filter vertices whose type is in a list of predefined types:

>>>
>>>

list_of_types = ["HR", "Finance", "Management"]

93
g.vs.select(type_in=list_of_types)

#doctest: +SKIP

If the operator is omitted, it defaults to eq. For instance, the following selector
selects vertices whose cluster property equals to 2:

Class VertexSeq

Package igraph

call(self, *args, **kwds)

Shorthand notation to select()
This method simply passes all its arguments to VertexSeq.select().
betweenness(*args, **kwds)
Proxy method to Graph.betweenness()
This method calls the betweenness() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.betweenness() for details.
bibcoupling(*args, **kwds)
Proxy method to Graph.bibcoupling()
This method calls the bibcoupling() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.bibcoupling() for details.
closeness(*args, **kwds)
Proxy method to Graph.closeness()
This method calls the closeness() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.closeness() for details.
cocitation(*args, **kwds)
Proxy method to Graph.cocitation()
This method calls the cocitation() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.cocitation() for details.
constraint(*args, **kwds)
Proxy method to Graph.constraint()
This method calls the constraint() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.constraint() for details.

Class VertexSeq

Package igraph

degree(*args, **kwds)
Proxy method to Graph.degree()
This method calls the degree() method of the Graph class restricted to this
sequence, and returns the result.
See Also: Graph.degree() for details.
delete(*args, **kwds)
Proxy method to Graph.delete_vertices()
This method calls the delete_vertices() method of the Graph class
restricted to this sequence, and returns the result.
See Also: Graph.delete_vertices() for details.
diversity(*args, **kwds)
Proxy method to Graph.diversity()
This method calls the diversity() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.diversity() for details.
eccentricity(*args, **kwds)
Proxy method to Graph.eccentricity()
This method calls the eccentricity() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.eccentricity() for details.
get_shortest_paths(*args, **kwds)
Proxy method to Graph.get_shortest_paths()
This method calls the get_shortest_paths() method of the Graph class
restricted to this sequence, and returns the result.
See Also: Graph.get_shortest_paths() for details.

Class VertexSeq

Package igraph

indegree(*args, **kwds)
Proxy method to Graph.indegree()
This method calls the indegree() method of the Graph class restricted to this
sequence, and returns the result.
See Also: Graph.indegree() for details.
is_minimal_separator(*args, **kwds)
Proxy method to Graph.is_minimal_separator()
This method calls the is_minimal_separator() method of the Graph class
restricted to this sequence, and returns the result.
See Also: Graph.is_minimal_separator() for details.
is_separator(*args, **kwds)
Proxy method to Graph.is_separator()
This method calls the is_separator() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.is_separator() for details.
isoclass(*args, **kwds)
Proxy method to Graph.isoclass()
This method calls the isoclass() method of the Graph class restricted to this
sequence, and returns the result.
See Also: Graph.isoclass() for details.
maxdegree(*args, **kwds)
Proxy method to Graph.maxdegree()
This method calls the maxdegree() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.maxdegree() for details.

Class VertexSeq

Package igraph

outdegree(*args, **kwds)
Proxy method to Graph.outdegree()
This method calls the outdegree() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.outdegree() for details.
pagerank(*args, **kwds)
Proxy method to Graph.pagerank()
This method calls the pagerank() method of the Graph class restricted to this
sequence, and returns the result.
See Also: Graph.pagerank() for details.
personalized_pagerank(*args, **kwds)
Proxy method to Graph.personalized_pagerank()
This method calls the personalized_pagerank() method of the Graph class
restricted to this sequence, and returns the result.
See Also: Graph.personalized_pagerank() for details.
shortest_paths(*args, **kwds)
Proxy method to Graph.shortest_paths()
This method calls the shortest_paths() method of the Graph class restricted
to this sequence, and returns the result.
See Also: Graph.shortest_paths() for details.
similarity_dice(*args, **kwds)
Proxy method to Graph.similarity_dice()
This method calls the similarity_dice() method of the Graph class
restricted to this sequence, and returns the result.
See Also: Graph.similarity_dice() for details.

Class EdgeSeq

Package igraph

similarity_jaccard(*args, **kwds)
Proxy method to Graph.similarity_jaccard()
This method calls the similarity_jaccard() method of the Graph class
restricted to this sequence, and returns the result.
See Also: Graph.similarity_jaccard() for details.
subgraph(*args, **kwds)
Proxy method to Graph.subgraph()
This method calls the subgraph() method of the Graph class restricted to this
sequence, and returns the result.
See Also: Graph.subgraph() for details.
Inherited from igraph.drawing.graph.VertexSeq
__delitem__(), __getitem__(), __init__(), __len__(), __new__(), __setitem__(),
attribute_names(), get_attribute_values(), set_attribute_values()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __reduce__(),
__reduce_ex__(), __repr__(), __setattr__(), __sizeof__(), __str__(),
__subclasshook__()
1.6.2

Properties

Name
Description
Inherited from igraph.drawing.graph.VertexSeq
graph, indices
Inherited from object
__class__

1.7

Class EdgeSeq

object
igraph._igraph.EdgeSeq
igraph.EdgeSeq
Class representing a sequence of edges in the graph.
98

Class EdgeSeq

Package igraph

This class is most easily accessed by the es field of the Graph object, which returns an
ordered sequence of all edges in the graph. The edge sequence can be refined by invoking
the EdgeSeq.select() method. EdgeSeq.select() can also be accessed by simply calling
the EdgeSeq object.
An alternative way to create an edge sequence referring to a given graph is to use the
constructor directly:
>>>
>>>
>>>

g = Graph.Full(3)
es = EdgeSeq(g)
restricted_es = EdgeSeq(g, [0, 1])

The individual edges can be accessed by indexing the edge sequence object. It can be used
as an iterable as well, or even in a list comprehension:
>>>

g=Graph.Full(3)
e in g.es:
print e.tuple

>>> for
...
...
(0, 1)
(0, 2)
(1, 2)
>>>

[max(e.tuple)

for

g.es]

[1, 2, 2]

The edge sequence can also be used as a dictionary where the keys are the attribute names.
The values corresponding to the keys are the values of the given attribute of every edge in
the graph:
>>>
>>>
...

g=Graph.Full(3)
for idx, e in enumerate(g.es):
e["weight"] = idx*(idx+1)

...
>>>

g.es["weight"]

[0, 2, 6]
>>>
>>>

g.es["weight"] = range(3)
g.es["weight"]

[0, 1, 2]

If you specify a sequence that is shorter than the number of edges in the EdgeSeq, the
sequence is reused:
>>>
>>>
>>>

g = Graph.Tree(7, 2)
g.es["color"] = ["red",
g.es["color"]

"green"]

[red, green, red, green, red, green]

You can even pass a single string or integer, it will be considered as a sequence of length 1:
99

Class EdgeSeq

>>>
>>>

g.es["color"] =
g.es["color"]

Package igraph

"red"

[red, red, red, red, red, red]

Some methods of the edge sequences are simply proxy methods to the corresponding methods
in the Graph object. One such example is EdgeSeq.is_multiple():
>>>
>>>

g=Graph(3, [(0,1), (1,0), (1,2)])

g.es.is_multiple()

[False, True, False]

>>>

g.es.is_multiple() == g.is_multiple()

True

1.7.1

Methods

attributes(self )
Returns the list of all the edge attributes in the graph associated to this edge
sequence.
find(self, *args, **kwds)
Returns the first edge of the edge sequence that matches some criteria.
The selection criteria are equal to the ones allowed by VertexSeq.select. See
VertexSeq.select for more details.
For instance, to find the first edge with weight larger than 5 in graph g:
>>>

g.es.find(weight_gt=5)

#doctest:+SKIP

Return Value
Edge
Overrides: igraph._igraph.EdgeSeq.find

100

Class EdgeSeq

Package igraph

select(self, *args, **kwds)

Selects a subset of the edge sequence based on some criteria
The selection criteria can be specified by the positional and the keyword
arguments. Positional arguments are always processed before keyword
arguments.
If the first positional argument is None, an empty sequence is returned.
If the first positional argument is a callable object, the object will be
called for every edge in the sequence. If it returns True, the edge will be
included, otherwise it will be excluded.
If the first positional argument is an iterable, it must return integers and
they will be considered as indices of the current edge set (NOT the whole
edge set of the graph the difference matters when one filters an edge set
that has already been filtered by a previous invocation of
EdgeSeq.select(). In this case, the indices do not refer directly to the
edges of the graph but to the elements of the filtered edge sequence.
If the first positional argument is an integer, all remaining arguments are
expected to be integers. They are considered as indices of the current
edge set again.
Keyword arguments can be used to filter the edges based on their attributes
and properties. The name of the keyword specifies the name of the attribute
and the filtering operator, they should be concatenated by an underscore (_)
character. Attribute names can also contain underscores, but operator names
dont, so the operator is always the largest trailing substring of the keyword
name that does not contain an underscore. Possible operators are:

For instance, if you want to filter edges with a numeric weight property larger
than 50, you have to write:
>>>

g.es.select(weight_gt=50)

#doctest: +SKIP

Similarly, to filter edges whose type is in a list of predefined types:

>>>
>>>

list_of_types = ["inhibitory", "excitatory"]

101
g.es.select(type_in=list_of_types)
#doctest:

+SKIP

If the operator is omitted, it defaults to eq. For instance, the following selector
selects edges whose type property is intracluster:

Class EdgeSeq

Package igraph

call(self, *args, **kwds)

Shorthand notation to select()
This method simply passes all its arguments to EdgeSeq.select().
count_multiple(*args, **kwds)
Proxy method to Graph.count_multiple()
This method calls the count_multiple() method of the Graph class restricted
to this sequence, and returns the result.
See Also: Graph.count_multiple() for details.
delete(*args, **kwds)
Proxy method to Graph.delete_edges()
This method calls the delete_edges() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.delete_edges() for details.
edge_betweenness(*args, **kwds)
Proxy method to Graph.edge_betweenness()
This method calls the edge_betweenness() method of the Graph class
restricted to this sequence, and returns the result.
See Also: Graph.edge_betweenness() for details.
is_loop(*args, **kwds)
Proxy method to Graph.is_loop()
This method calls the is_loop() method of the Graph class restricted to this
sequence, and returns the result.
See Also: Graph.is_loop() for details.
is_multiple(*args, **kwds)
Proxy method to Graph.is_multiple()
This method calls the is_multiple() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.is_multiple() for details.

102

Class ARPACKOptions

Package igraph

is_mutual(*args, **kwds)
Proxy method to Graph.is_mutual()
This method calls the is_mutual() method of the Graph class restricted to
this sequence, and returns the result.
See Also: Graph.is_mutual() for details.
subgraph(*args, **kwds)
Proxy method to Graph.subgraph_edges()
This method calls the subgraph_edges() method of the Graph class restricted
to this sequence, and returns the result.
See Also: Graph.subgraph_edges() for details.
Inherited from igraph._igraph.EdgeSeq
__delitem__(), __getitem__(), __init__(), __len__(), __new__(), __setitem__(),
attribute_names(), get_attribute_values(), is_all(), set_attribute_values()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __reduce__(),
__reduce_ex__(), __repr__(), __setattr__(), __sizeof__(), __str__(),
__subclasshook__()
1.7.2

Properties

Name
Inherited from igraph._igraph.EdgeSeq
graph, indices
Inherited from object
__class__

1.8

Description

Class ARPACKOptions

object
igraph.ARPACKOptions
Class representing the parameters of the ARPACK module.
ARPACK is a Fortran implementation of the implicitly restarted Arnoldi method, an algo-

103

Class ARPACKOptions

Package igraph

rithm for calculating some of the eigenvalues and eigenvectors of a given matrix. igraph uses
this package occasionally, and this class can be used to fine-tune the behaviour of ARPACK
in such cases.
The class has several attributes which are not documented here, since they are usually of
marginal use to the ordinary user. See the source code of the original ARPACK Fortran
package (especially the file dsaupd.f) for a detailed explanation of the parameters. Only
the most basic attributes are explained here. Most of them are read only unless stated
otherwise.
bmat: type of the eigenproblem solved. I means standard eigenproblem (A*x =
lambda*x), G means generalized eigenproblem (A*x = lambda*B*x).
n: dimension of the eigenproblem
tol: precision. If less than or equal to zero, the standard machine precision is used as
computed by the LAPACK utility called dlamch. This can be modified.
mxiter: maximum number of update iterations to take. This can be modified. You can
also use maxiter.
iter: actual number of update iterations taken
numop: total number of OP*x operations
numopb: total number of B*x operations if bmat is G
numreo: total number of steps of re-orthogonalization
1.8.1

Methods

__new__(T, S, ...)
Return Value
a new object with type S, a subtype of T
Overrides: object.__new__
__str__(x )
str(x)
Overrides: object.__str__
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __init__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__subclasshook__()
1.8.2

Properties

104

Class Edge

Package igraph

Name
Inherited from object
__class__

1.9

Description

Class BFSIter

object
igraph.BFSIter
igraph BFS iterator object
1.9.1

Methods

__iter__(x )
iter(x)
next(x )
Return Value
the next value, or raise StopIteration
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __init__(),
__new__(), __reduce__(), __reduce_ex__(), __repr__(), __setattr__(),
__sizeof__(), __str__(), __subclasshook__()
1.9.2

Properties

Name
Inherited from object
__class__

1.10

Description

Class Edge

object
igraph.Edge

105

Class Edge

Package igraph

Class representing a single edge in a graph.

The edge is referenced by its index, so if the underlying graph changes, the semantics of the
edge object might change as well (if the edge indices are altered in the original graph).
The attributes of the edge can be accessed by using the edge as a hash:
>>>
>>>

e["weight"] = 2
print e["weight"]

#doctest: +SKIP
#doctest: +SKIP

1.10.1

Methods

__delitem__(x, y)
del x[y]
__eq__(x, y)
x==y
__ge__(x, y)
x>=y
__getitem__(x, y)
x[y]
__gt__(x, y)
x>y
__hash__(x )
hash(x)
Overrides: object.__hash__
__le__(x, y)
x<=y
__len__(x )
len(x)

106

Class Edge

Package igraph

__lt__(x, y)
x<y
__ne__(x, y)
x!=y
__repr__(x )
repr(x)
Overrides: object.__repr__
__setitem__(x, i, y)
x[i]=y
attribute_names()
Returns the list of edge attribute names
Return Value
list
attributes()
Returns a dict of attribute names and values for the edge
Return Value
dict
count_multiple(...)
Proxy method to Graph.count_multiple()
This method calls the count_multiple method of the Graph class with this
edge as the first argument, and returns the result.
See Also: Graph.count_multiple() for details.
delete(...)
Proxy method to Graph.delete_edges()
This method calls the delete_edges method of the Graph class with this edge
as the first argument, and returns the result.
See Also: Graph.delete_edges() for details.

107

Class Edge

Package igraph

is_loop(...)
Proxy method to Graph.is_loop()
This method calls the is_loop method of the Graph class with this edge as the
first argument, and returns the result.
See Also: Graph.is_loop() for details.
is_multiple(...)
Proxy method to Graph.is_multiple()
This method calls the is_multiple method of the Graph class with this edge as
the first argument, and returns the result.
See Also: Graph.is_multiple() for details.
is_mutual(...)
Proxy method to Graph.is_mutual()
This method calls the is_mutual method of the Graph class with this edge as
the first argument, and returns the result.
See Also: Graph.is_mutual() for details.
update_attributes(E, **F )
Updates the attributes of the edge from dict/iterable E and F.
If E has a keys() method, it does: for k in E: self[k] = E[k]. If E lacks
a keys() method, it does: for (k, v) in E: self[k] = v. In either case,
this is followed by: for k in F: self[k] = F[k].
This method thus behaves similarly to the update() method of Python
dictionaries.
Return Value
None
Inherited from object
__delattr__(), __format__(), __getattribute__(), __init__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __str__(),
__subclasshook__()
1.10.2

Properties

108

Class GraphBase

Package igraph

Name
graph
index
source
target
tuple

Description
The graph the edge belongs to
Index of this edge
Source node index of this edge
Target node index of this edge
Source and target node index of this edge as a
tuple

Inherited from object

__class__

1.11

Class GraphBase

object
igraph.GraphBase
Known Subclasses: igraph.Graph
Low-level representation of a graph.
Dont use it directly, use igraph.Graph instead.

109

Class GraphBase

1.11.1

Package igraph

Methods

Adjacency(matrix, mode=ADJ_DIRECTED)
Generates a graph from its adjacency matrix.
Parameters
matrix: the adjacency matrix
mode:

the mode to be used. Possible values are:

ADJ_DIRECTED - the graph will be directed and a matrix
element gives the number of edges between two vertex.
ADJ_UNDIRECTED - alias to ADJ_MAX for convenience.
ADJ_MAX - undirected graph will be created and the
number of edges between vertex i and j is max(A(i,j),
A(j,i))
ADJ_MIN - like ADJ_MAX, but with min(A(i,j), A(j,i))
ADJ_PLUS - like ADJ_MAX, but with A(i,j) + A(j,i)
ADJ_UPPER - undirected graph with the upper right
triangle of the matrix (including the diagonal)
ADJ_LOWER - undirected graph with the lower left
triangle of the matrix (including the diagonal)
These values can also be given as strings without the ADJ
prefix.

110

Class GraphBase

Package igraph

Asymmetric_Preference(n, type_dist_matrix, pref_matrix,

attribute=None, loops=False)
Generates a graph based on asymmetric vertex types and connection
probabilities.
This is the asymmetric variant of Graph.Preference. A given number of
vertices are generated. Every vertex is assigned to an "incoming" and an
"outgoing" vertex type according to the given joint type probabilities. Finally,
every vertex pair is evaluated and a directed edge is created between them
with a probability depending on the "outgoing" type of the source vertex and
the "incoming" type of the target vertex.
Parameters
n:

the number of vertices in the graph

type_dist_matrix: matrix giving the joint distribution of vertex

types
pref_matrix:

matrix giving the connection probabilities for

different vertex types.

attribute:

the vertex attribute name used to store the

vertex types. If None, vertex types are not
stored.

loops:

whether loop edges are allowed.

Atlas(idx )
Generates a graph from the Graph Atlas.
Parameters
idx: The index of the graph to be generated. Indices start from
zero, graphs are listed:
1. in increasing order of number of vertices;
2. for a fixed number of vertices, in increasing order of the
number of edges;
3. for fixed numbers of vertices and edges, in increasing order
of the degree sequence, for example 111223 < 112222;
4. for fixed degree sequence, in increasing number of
automorphisms.
Reference: An Atlas of Graphs by Ronald C. Read and Robin J. Wilson,
Oxford University Press, 1998.

111

Class GraphBase

Package igraph

Barabasi(n, m, outpref =False, directed =False, power =1, zero_appeal =1,

implementation="psumtree", start_from=None)
Generates a graph based on the Barabasi-Albert model.
Parameters
n:

the number of vertices

either the number of outgoing edges generated for

each vertex or a list containing the number of
outgoing edges for each vertex explicitly.

outpref:

True if the out-degree of a given vertex should

also increase its citation probability (as well as its
in-degree), but it defaults to False.

directed:

True if the generated graph should be directed

(default: False).

power:

the power constant of the nonlinear model. It can

be omitted, and in this case the usual linear
model will be used.

zero_appeal:

the attractivity of vertices with degree zero.

implementation: the algorithm to use to generate the network.

Possible values are:
"bag": the algorithm that was the default in
igraph before 0.6. It works by putting the ids
of the vertices into a bag (multiset) exactly as
many times as their in-degree, plus once more.
The required number of cited vertices are then
drawn from the bag with replacement. It
works only for power =1 and zero_appeal =1.
"psumtree": this algorithm uses a partial
prefix-sum tree to generate the graph. It does
not generate multiple edges and it works for
any values of power and zero_appeal.
"psumtree_multiple": similar to
"psumtree", but it will generate multiple
edges as well. igraph before 0.6 used this
algorithm for power s other than 1.
start_from:

if given and not None, this must be another Graph

object. igraph will use this graph as a starting
point for the preferential attachment model.

Reference: Barabasi, A-L and Albert, R. 1999. Emergence of scaling in

random networks. Science, 286 509-512.

112

Class GraphBase

Package igraph

De_Bruijn(m, n)
Generates a de Bruijn graph with parameters (m, n)
A de Bruijn graph represents relationships between strings. An alphabet of m
letters are used and strings of length n are considered. A vertex corresponds
to every possible string and there is a directed edge from vertex v to vertex w
if the string of v can be transformed into the string of w by removing its first
letter and appending a letter to it.
Please note that the graph will have m^n vertices and even more edges, so
probably you dont want to supply too big numbers for m and n.
Parameters
m: the size of the alphabet
n: the length of the strings

113

Class GraphBase

Package igraph

Degree_Sequence(out, in=None, method ="simple")

Generates a graph with a given degree sequence.
Parameters
out:
the out-degree sequence for a directed graph. If the
in-degree sequence is omitted, the generated graph will be
undirected, so this will be the in-degree sequence as well
in:

the in-degree sequence for a directed graph. If omitted, the

generated graph will be undirected.

method: the generation method to be used. One of the following:

"simple" simple generator that sometimes generates
loop edges and multiple edges. The generated graph is
not guaranteed to be connected.
"no_multiple" similar to "simple" but avoids the
generation of multiple and loop edges at the expense of
increased time complexity. The method will re-start the
generation every time it gets stuck in a configuration
where it is not possible to insert any more edges
without creating loops or multiple edges, and there is
no upper bound on the number of iterations, but it will
succeed eventually if the input degree sequence is
graphical and throw an exception if the input degree
sequence is not graphical.
"vl" a more sophisticated generator that can sample
undirected, connected simple graphs uniformly. It uses
Monte-Carlo methods to randomize the graphs. This
generator should be favoured if undirected and
connected graphs are to be generated and execution
time is not a concern. igraph uses the original
implementation of Fabien Viger; see the following URL
and the paper cited on it for the details of the
algorithm:
http://www-rp.lip6.fr/~latapy/FV/generation.html .

114

Class GraphBase

Package igraph

Erdos_Renyi(n, p, m, directed =False, loops=False)

Generates a graph based on the Erdos-Renyi model.
Parameters
n:

the number of vertices.

the probability of edges. If given, m must be missing.

the number of edges. If given, p must be missing.

directed: whether to generate a directed graph.

loops:

whether self-loops are allowed.

Establishment(n, k, type_dist, pref_matrix, directed =False)

Generates a graph based on a simple growing model with vertex types.
A single vertex is added at each time step. This new vertex tries to connect to
k vertices in the graph. The probability that such a connection is realized
depends on the types of the vertices involved.
Parameters
n:

the number of vertices in the graph

the number of connections tried in each step

type_dist:

list giving the distribution of vertex types

pref_matrix: matrix (list of lists) giving the connection

probabilities for different vertex types
directed:

whether to generate a directed graph.

Famous(name)
Generates a famous graph based on its name.
Several famous graphs are known to igraph including (but not limited to) the
Chvatal graph, the Petersen graph or the Tutte graph. This method generates
one of them based on its name (case insensitive). See the documentation of
the C interface of igraph for the names available: http://igraph.org/doc/c.
Parameters
name: the name of the graph to be generated.

115

Class GraphBase

Package igraph

Forest_Fire(n, fw_prob, bw_factor =0.0, ambs=1, directed =False)

Generates a graph based on the forest fire model
The forest fire model is a growin graph model. In every time step, a new
vertex is added to the graph. The new vertex chooses an ambassador (or more
than one if ambs>1 ) and starts a simulated forest fire at its ambassador(s).
The fire spreads through the edges. The spreading probability along an edge is
given by fw_prob. The fire may also spread backwards on an edge by
probability fw_prob * bw_factor. When the fire ended, the newly added
vertex connects to the vertices burned in the previous fire.
Parameters
n:
fw_prob:

the number of vertices in the graph

forward burning probability

bw_factor: ratio of backward and forward burning probability

ambs:

number of ambassadors chosen in each step

directed: whether the graph will be directed

Full(n, directed =False, loops=False)
Generates a full graph (directed or undirected, with or without loops).
Parameters
n:

the number of vertices.

directed: whether to generate a directed graph.

loops:

whether self-loops are allowed.

Full_Citation(n, directed =False)

Generates a full citation graph
A full citation graph is a graph where the vertices are indexed from 0 to n-1
and vertex i has a directed edge towards all vertices with an index less than i.
Parameters
n:

the number of vertices.

directed: whether to generate a directed graph.

116

Class GraphBase

Package igraph

Growing_Random(n, m, directed =False, citation=False)

Generates a growing random graph.
Parameters
n:
m:

The number of vertices in the graph

The number of edges to add in each step (after adding a
new vertex)

directed: whether the graph should be directed.

citation: whether the new edges should originate from the most
recently added vertex.
Isoclass(n, class, directed =False)
Generates a graph with a given isomorphy class.
Parameters
n:
class:

the number of vertices in the graph (3 or 4)

the isomorphy class

directed: whether the graph should be directed.

K_Regular(n, k, directed =False, multiple=False)
Generates a k-regular random graph
A k-regular random graph is a random graph where each vertex has degree k.
If the graph is directed, both the in-degree and the out-degree of each vertex
will be k.
Parameters
n:
k:

The number of vertices in the graph

The degree of each vertex if the graph is undirected, or
the in-degree and out-degree of each vertex if the graph
is directed

directed: whether the graph should be directed.

multiple: whether it is allowed to create multiple edges.

117

Class GraphBase

Package igraph

Kautz(m, n)
Generates a Kautz graph with parameters (m, n)
A Kautz graph is a labeled graph, vertices are labeled by strings of length n+1
above an alphabet with m+1 letters, with the restriction that every two
consecutive letters in the string must be different. There is a directed edge
from a vertex v to another vertex w if it is possible to transform the string of v
into the string of w by removing the first letter and appending a letter to it.
Parameters
m: the size of the alphabet minus one
n: the length of the strings minus one
LCF(n, shifts, repeats)
Generates a graph from LCF notation.
LCF is short for Lederberg-Coxeter-Frucht, it is a concise notation for
3-regular Hamiltonian graphs. It consists of three parameters, the number of
vertices in the graph, a list of shifts giving additional edges to a cycle
backbone and another integer giving how many times the shifts should be
performed. See http://mathworld.wolfram.com/LCFNotation.html for details.
Parameters
n:

the number of vertices

shifts: the shifts in a list or tuple

repeats: the number of repeats
Lattice(dim, nei=1, directed =False, mutual =True, circular =True)
Generates a regular lattice.
Parameters
dim:
nei:

list with the dimensions of the lattice

value giving the distance (number of steps) within which
two vertices will be connected.

directed: whether to create a directed graph.

mutual:

whether to create all connections as mutual in case of a

directed graph.

circular: whether the generated lattice is periodic.

118

Class GraphBase

Package igraph

Preference(n, type_dist, pref_matrix, attribute=None, directed =False,

loops=False)
Generates a graph based on vertex types and connection probabilities.
This is practically the nongrowing variant of Graph.Establishment. A given
number of vertices are generated. Every vertex is assigned to a vertex type
according to the given type probabilities. Finally, every vertex pair is
evaluated and an edge is created between them with a probability depending
on the types of the vertices involved.
Parameters
n:

the number of vertices in the graph

type_dist:

list giving the distribution of vertex types

pref_matrix: matrix giving the connection probabilities for

different vertex types.
attribute:

the vertex attribute name used to store the vertex

types. If None, vertex types are not stored.

directed:

whether to generate a directed graph.

loops:

whether loop edges are allowed.

Read_DIMACS(f, directed =False)

Reads a graph from a file conforming to the DIMACS minimum-cost flow file
format.
For the exact description of the format, see
http://lpsolve.sourceforge.net/5.5/DIMACS.htm
Restrictions compared to the official description of the format:
igraphs DIMACS reader requires only three fields in an arc definition,
describing the edges source and target node and its capacity.
Source vertices are identified by s in the FLOW field, target vertices are
identified by t.
Node indices start from 1. Only a single source and target node is allowed.
Parameters
f:

the name of the file or a Python file handle

directed: whether the generated graph should be directed.

Return Value
the generated graph, the source and the target of the flow and the
edge capacities in a tuple

119

Class GraphBase

Package igraph

Read_DL(f, directed =True)

Reads an UCINET DL file and creates a graph based on it.
Parameters
f:

the name of the file or a Python file handle

directed: whether the generated graph should be directed.

Read_Edgelist(f, directed =True)
Reads an edge list from a file and creates a graph based on it.
Please note that the vertex indices are zero-based.
Parameters
f:

the name of the file or a Python file handle

directed: whether the generated graph should be directed.

Read_GML(f )
Reads a GML file and creates a graph based on it.
Parameters
f: the name of the file or a Python file handle
Read_GraphDB(f, directed =False)
Reads a GraphDB format file and creates a graph based on it.
GraphDB is a binary format, used in the graph database for isomorphism
testing (see http://amalfi.dis.unina.it/graph/ ).
Parameters
f:

the name of the file or a Python file handle

directed: whether the generated graph should be directed.

Read_GraphML(f, directed =True, index =0)
Reads a GraphML format file and creates a graph based on it.
Parameters
f:
the name of the file or a Python file handle
index: if the GraphML file contains multiple graphs, specifies the
one that should be loaded. Graph indices start from zero, so
if you want to load the first graph, specify 0 here.

120

Class GraphBase

Package igraph

Read_Lgl(f, names=True, weights="if_present", directed =True)

Reads an .lgl file used by LGL.
It is also useful for creating graphs from "named" (and optionally weighted)
edge lists.
This format is used by the Large Graph Layout program. See the
documentation of LGLa regarding the exact format description.
LGL originally cannot deal with graphs containing multiple or loop edges, but
this condition is not checked here, as igraph is happy with these.
Parameters
f:
names:

the name of the file or a Python file handle

If True, the vertex names are added as a vertex attribute
called name.

weights: If True, the edge weights are added as an edge attribute

called weight, even if there are no weights in the file. If
False, the edge weights are never added, even if they are
present. "auto" or "if_present" means that weights
are added if there is at least one weighted edge in the
input file, but they are not added otherwise.
directed: whether the graph being created should be directed
a http://bioinformatics.icmb.utexas.edu/lgl/

121

Class GraphBase

Package igraph

Read_Ncol(f, names=True, weights="if_present", directed =True)

Reads an .ncol file used by LGL.
It is also useful for creating graphs from "named" (and optionally weighted)
edge lists.
This format is used by the Large Graph Layout program. See the
documentation of LGLa regarding the exact format description.
LGL originally cannot deal with graphs containing multiple or loop edges, but
this condition is not checked here, as igraph is happy with these.
Parameters
f:
names:

the name of the file or a Python file handle

If True, the vertex names are added as a vertex attribute
called name.

weights: If True, the edge weights are added as an edge attribute

Read_Pajek(f )
Reads a Pajek format file and creates a graph based on it.
Parameters
f: the name of the file or a Python file handle

122

Class GraphBase

Package igraph

Recent_Degree(n, m, window, outpref =False, directed =False, power =1)

Generates a graph based on a stochastic model where the probability of an
edge gaining a new node is proportional to the edges gained in a given time
window.
Parameters
n:

the number of vertices

either the number of outgoing edges generated for each

vertex or a list containing the number of outgoing edges
for each vertex explicitly.

window:

size of the window in time steps

outpref: True if the out-degree of a given vertex should also

increase its citation probability (as well as its in-degree),
but it defaults to False.
directed: True if the generated graph should be directed (default:
False).
power:

the power constant of the nonlinear model. It can be

omitted, and in this case the usual linear model will be
used.

Ring(n, directed =False, mutual =False, circular =True)

Generates a ring graph.
Parameters
n:

the number of vertices in the ring

directed: whether to create a directed ring.

mutual:

whether to create mutual edges in a directed ring.

circular: whether to create a closed ring.

123

Class GraphBase

Package igraph

SBM(n, pref_matrix, block_sizes, directed =False, loops=False)

Generates a graph based on a stochastic blockmodel.
A given number of vertices are generated. Every vertex is assigned to a vertex
type according to the given block sizes. Vertices of the same type will be
assigned consecutive vertex IDs. Finally, every vertex pair is evaluated and an
edge is created between them with a probability depending on the types of the
vertices involved. The probabilities are taken from the preference matrix.
Parameters
n:

the number of vertices in the graph

pref_matrix: matrix giving the connection probabilities for

different vertex types.
block_sizes: list giving the number of vertices in each block; must
sum up to n.
directed:

whether to generate a directed graph.

loops:

whether loop edges are allowed.

Star(n, mode="undirected", center =0)

Generates a star graph.
Parameters
n:
the number of vertices in the graph
mode:

Gives the type of the star graph to create. Should be either

"in", "out", "mutual" or "undirected"

center: Vertex ID for the central vertex in the star.

124

Class GraphBase

Package igraph

Static_Fitness(m, fitness_out, fitness_in=None, loops=False,

multiple=False)
Generates a non-growing graph with edge probabilities proportional to node
fitnesses.
The algorithm randomly selects vertex pairs and connects them until the given
number of edges are created. Each vertex is selected with a probability
proportional to its fitness; for directed graphs, a vertex is selected as a source
proportional to its out-fitness and as a target proportional to its in-fitness.
Parameters
m:

the number of edges in the graph

fitness_out: a numeric vector with non-negative entries, one for

each vertex. These values represent the fitness scores
(out-fitness scores for directed graphs). fitness is an
alias of this keyword argument.
fitness_in: a numeric vector with non-negative entries, one for
each vertex. These values represent the in-fitness
scores for directed graphs. For undirected graphs,
this argument must be None.
loops:

whether loop edges are allowed.

multiple:

whether multiple edges are allowed.

Return Value
a directed or undirected graph with the prescribed power-law degree
distributions.

125

Class GraphBase

Package igraph

Static_Power_Law(n, m, exponent_out, exponent_in=-1, loops=False,

multiple=False, finite_size_correction=True)
Generates a non-growing graph with prescribed power-law degree distributions.
Parameters
n:

the number of vertices in the graph

the number of edges in the graph

exponent_out:

the exponent of the out-degree

distribution, which must be between 2
and infinity (inclusive). When
exponent_in is not given or negative,
the graph will be undirected and this
parameter specifies the degree
distribution. exponent is an alias to this
keyword argument.

exponent_in:

the exponent of the in-degree

distribution, which must be between 2
and infinity (inclusive) It can also be
negative, in which case an undirected
graph will be generated.

loops:

whether loop edges are allowed.

multiple:

whether multiple edges are allowed.

finite_size_correction: whether to apply a finite-size correction

to the generated fitness values for
exponents less than 3. See the paper of
Cho et al for more details.
Return Value
a directed or undirected graph with the prescribed power-law degree
distributions.
Reference:
Goh K-I, Kahng B, Kim D: Universal behaviour of load
distribution in scale-free networks. Phys Rev Lett
87(27):278701, 2001.
Cho YS, Kim JS, Park J, Kahng B, Kim D: Percolation
transitions in scale-free networks under the Achlioptas process.
Phys Rev Lett 103:135702, 2009.

126

Class GraphBase

Package igraph

Tree(n, children, type=TREE_UNDIRECTED)

Generates a tree in which almost all vertices have the same number of children.
Parameters
n:

the number of vertices in the graph

children: the number of children of a vertex in the graph

type:

determines whether the tree should be directed, and if

this is the case, also its orientation. Must be one of
TREE_IN, TREE_OUT and TREE_UNDIRECTED.

Watts_Strogatz(dim, size, nei, p, loops=False, multiple=False)

Parameters
dim:

the dimension of the lattice

size:

the size of the lattice along all dimensions

nei:

value giving the distance (number of steps) within which

two vertices will be connected.

rewiring probability

loops:

specifies whether loop edges are allowed

multiple: specifies whether multiple edges are allowed

See Also: Lattice(), rewire(), rewire_edges() if more flexibility is needed
Reference: Duncan J Watts and Steven H Strogatz: Collective dynamics of
small world networks, Nature 393, 440-442, 1998

127

Class GraphBase

Package igraph

Weighted_Adjacency(matrix, mode=ADJ_DIRECTED, attr ="weight",

loops=True)
Generates a graph from its adjacency matrix.
Parameters
matrix: the adjacency matrix
mode:

the mode to be used. Possible values are:

attr:

the name of the edge attribute that stores the edge weights.

loops: whether to include loop edges. When False, the diagonal

of the adjacency matrix will be ignored.
__and__(x, y)
x&y
__delitem__(x, y)
del x[y]
__getitem__(x, y)
x[y]
__init__(...)
x.__init__(...) initializes x; see help(type(x)) for signature
Overrides: object.__init__

128

Class GraphBase

Package igraph

__invert__(x )
~x
__new__(T, S, ...)
Return Value
a new object with type S, a subtype of T
Overrides: object.__new__
__or__(x, y)
x|y
__rand__(x, y)
y&x
__ror__(x, y)
y|x
__setitem__(x, i, y)
x[i]=y
__str__(x )
str(x)
Overrides: object.__str__
add_edges(es)
Adds edges to the graph.
Parameters
es: the list of edges to be added. Every edge is represented with a
tuple, containing the vertex IDs of the two endpoints. Vertices
are enumerated from zero.
add_vertices(n)
Adds vertices to the graph.
Parameters
n: the number of vertices to be added

129

Class GraphBase

Package igraph

all_minimal_st_separators()
Returns a list containing all the minimal s-t separators of a graph.
A minimal separator is a set of vertices whose removal disconnects the graph,
while the removal of any subset of the set keeps the graph connected.
Return Value
a list where each item lists the vertex indices of a given minimal s-t
separator.
Reference: Anne Berry, Jean-Paul Bordat and Olivier Cogis: Generating all
the minimal separators of a graph. In: Peter Widmayer, Gabriele Neyer and
Stephan Eidenbenz (eds.): Graph-theoretic concepts in computer science,
1665, 167172, 1999. Springer.
all_st_cuts(source, target)
Returns all the cuts between the source and target vertices in a directed graph.
This function lists all edge-cuts between a source and a target vertex. Every
cut is listed exactly once.
Parameters
source: the source vertex ID
target: the target vertex ID
Return Value
a tuple where the first element is a list of lists of edge IDs
representing a cut and the second element is a list of lists of vertex
IDs representing the sets of vertices that were separated by the cuts.
Attention: this function has a more convenient interface in class Graph which
wraps the result in a list of Cut objects. It is advised to use that.
all_st_mincuts(source, target)
Returns all minimum cuts between the source and target vertices in a directed
graph.
Parameters
source: the source vertex ID
target: the target vertex ID
Attention: this function has a more convenient interface in class Graph which
wraps the result in a list of Cut objects. It is advised to use that.

130

Class GraphBase

Package igraph

are_connected(v1, v2 )
Decides whether two given vertices are directly connected.
Parameters
v1: the first vertex
v2: the second vertex
Return Value
True if there exists an edge from v1 to v2, False otherwise.
articulation_points()
Returns the list of articulation points in the graph.
A vertex is an articulation point if its removal increases the number of
connected components in the graph.

131

Class GraphBase

Package igraph

assortativity(types1, types2 =None, directed =True)

Returns the assortativity of the graph based on numeric properties of the
vertices.
This coefficient is basically the correlation between the actual connectivity
patterns of the vertices and the pattern expected from the disribution of the
vertex types.
See equation (21) in Newman MEJ: Mixing patterns in networks, Phys Rev E
67:026126 (2003) for the proper definition. The actual calculation is performed
using equation (26) in the same paper for directed graphs, and equation (4) in
Newman MEJ: Assortative mixing in networks, Phys Rev Lett 89:208701
(2002) for undirected graphs.
Parameters
types1:

types2:

vertex types in a list or the name of a vertex attribute

holding vertex types. Types are ideally denoted by
numeric values.
in directed assortativity calculations, each vertex can
have an out-type and an in-type. In this case, types1
contains the out-types and this parameter contains the
in-types in a list or the name of a vertex attribute. If
None, it is assumed to be equal to types1.

directed: whether to consider edge directions or not.

Return Value
the assortativity coefficient
Reference:
Newman MEJ: Mixing patterns in networks, Phys Rev E
67:026126, 2003.
Newman MEJ: Assortative mixing in networks, Phys Rev Lett
89:208701, 2002.@see: assortativity_degree() when the
types are the vertex degrees

132

Class GraphBase

Package igraph

assortativity_degree(directed =True)
Returns the assortativity of a graph based on vertex degrees.
See assortativity() for the details. assortativity_degree() simply calls
assortativity() with the vertex degrees as types.
Parameters
directed: whether to consider edge directions for directed graphs
or not. This argument is ignored for undirected graphs.
Return Value
the assortativity coefficient
See Also: assortativity()
assortativity_nominal(types, directed =True)
Returns the assortativity of the graph based on vertex categories.
Assuming that the vertices belong to different categories, this function
calculates the assortativity coefficient, which specifies the extent to which the
connections stay within categories. The assortativity coefficient is one if all the
connections stay within categories and minus one if all the connections join
vertices of different categories. For a randomly connected network, it is
asymptotically zero.
See equation (2) in Newman MEJ: Mixing patterns in networks, Phys Rev E
67:026126 (2003) for the proper definition.
Parameters
types:

vertex types in a list or the name of a vertex attribute

holding vertex types. Types should be denoted by
numeric values.

directed: whether to consider edge directions or not.

Return Value
the assortativity coefficient
Reference: Newman MEJ: Mixing patterns in networks, Phys Rev E
67:026126, 2003.
attributes()
Return Value
the attribute name list of the graph

133

Class GraphBase

Package igraph

authority_score(weights=None, scale=True, arpack_options=None,

return_eigenvalue=False)
Calculates Kleinbergs authority score for the vertices of the graph
Parameters
weights:

edge weights to be used. Can be a sequence or

iterable or even an edge attribute name.

scale:

whether to normalize the scores so that the

largest one is 1.

arpack_options:

an ARPACKOptions object used to fine-tune

the ARPACK eigenvector calculation. If
omitted, the module-level variable called
arpack_options is used.

return_eigenvalue: whether to return the largest eigenvalue

Return Value
the authority scores in a list and optionally the largest eigenvalue as
a second member of a tuple
See Also: hub_score()
average_path_length(directed =True, unconn=True)
Calculates the average path length in a graph.
Parameters
directed: whether to consider directed paths in case of a directed
graph. Ignored for undirected graphs.
unconn:

what to do when the graph is unconnected. If True, the

average of the geodesic lengths in the components is
calculated. Otherwise for all unconnected vertex pairs, a
path length equal to the number of vertices is used.

Return Value
the average path length in the graph

134

Class GraphBase

Package igraph

betweenness(vertices=None, directed =True, cutoff =None, weights=None,

nobigint=True)
Calculates or estimates the betweenness of vertices in a graph.
Keyword arguments:
Parameters
vertices: the vertices for which the betweennesses must be
returned. If None, assumes all of the vertices in the
graph.
directed: whether to consider directed paths.
cutoff:

if it is an integer, only paths less than or equal to this

length are considered, effectively resulting in an
estimation of the betweenness for the given vertices. If
None, the exact betweenness is returned.

weights: edge weights to be used. Can be a sequence or iterable or

even an edge attribute name.
nobigint: if True, igraph uses the longest available integer type on
the current platform to count shortest paths. For some
large networks that have a specific structure, the counters
may overflow. To prevent this, use nobigint=False,
which forces igraph to use arbitrary precision integers at
the expense of increased computation time.
Return Value
the (possibly estimated) betweenness of the given vertices in a list
bfs(vid, mode=OUT)
Conducts a breadth first search (BFS) on the graph.
Parameters
vid: the root vertex ID
mode: either IN or OUT or ALL, ignored for undirected graphs.
Return Value
a tuple with the following items:
The vertex IDs visited (in order)
The start indices of the layers in the vertex list
The parent of every vertex in the BFS

135

Class GraphBase

Package igraph

bfsiter(vid, mode=OUT, advanced =False)

Constructs a breadth first search (BFS) iterator of the graph.
Parameters
vid:
mode:

the root vertex ID

either IN or OUT or ALL.

advanced: if False, the iterator returns the next vertex in BFS

order in every step. If True, the iterator returns the
distance of the vertex from the root and the parent of
the vertex in the BFS tree as well.
Return Value
the BFS iterator as an igraph.BFSIter object.
bibcoupling(vertices=None)
Calculates bibliographic coupling scores for given vertices in a graph.
Parameters
vertices: the vertices to be analysed. If None, all vertices will be
considered.
Return Value
bibliographic coupling scores for all given vertices in a matrix.
biconnected_components(return_articulation_points=True)
Calculates the biconnected components of the graph.
Parameters
return_articulation_points: whether to return the articulation
points as well
Return Value
a list of lists containing edge indices making up spanning trees of the
biconnected components (one spanning tree for each component) and
optionally the list of articulation points
bipartite_projection(types, multiplicity=True, probe1 =-1, which=-1)
Internal function, undocumented.
See Also: Graph.bipartite_projection()
bipartite_projection_size(types)
Internal function, undocumented.
See Also: Graph.bipartite_projection_size()
136

Class GraphBase

Package igraph

canonical_permutation(sh="fm")
Calculates the canonical permutation of a graph using the BLISS isomorphism
algorithm.
Passing the permutation returned here to Graph.permute_vertices() will
transform the graph into its canonical form.
See http://www.tcs.hut.fi/Software/bliss/index.html for more information
about the BLISS algorithm and canonical permutations.
Parameters
sh: splitting heuristics for graph as a case-insensitive string, with
the following possible values:
"f": first non-singleton cell
"fl": first largest non-singleton cell
"fs": first smallest non-singleton cell
"fm": first maximally non-trivially connected non-singleton
cell
"flm": largest maximally non-trivially connected
non-singleton cell
"fsm": smallest maximally non-trivially connected
non-singleton cell

Return Value
a permutation vector containing vertex IDs. Vertex 0 in the original
graph will be mapped to an ID contained in the first element of this
vector; vertex 1 will be mapped to the second and so on.
clique_number()
Returns the clique number of the graph.
The clique number of the graph is the size of the largest clique.
See Also: largest_cliques() for the largest cliques.

137

Class GraphBase

Package igraph

cliques(min=0, max =0)

Returns some or all cliques of the graph as a list of tuples.
A clique is a complete subgraph a set of vertices where an edge is present
between any two of them (excluding loops)
Parameters
min: the minimum size of cliques to be returned. If zero or negative,
no lower bound will be used.
max: the maximum size of cliques to be returned. If zero or
negative, no upper bound will be used.

138

Class GraphBase

Package igraph

closeness(vertices=None, mode=ALL, cutoff =None, weights=None,

normalized =True)
Calculates the closeness centralities of given vertices in a graph.
The closeness centerality of a vertex measures how easily other vertices can be
reached from it (or the other way: how easily it can be reached from the other
vertices). It is defined as the number of the number of vertices minus one
divided by the sum of the lengths of all geodesics from/to the given vertex.
If the graph is not connected, and there is no path between two vertices, the
number of vertices is used instead the length of the geodesic. This is always
longer than the longest possible geodesic.
Parameters
vertices:

the vertices for which the closenesses must be

returned. If None, uses all of the vertices in the graph.

mode:

must be one of IN, OUT and ALL. IN means that the

length of the incoming paths, OUT means that the
length of the outgoing paths must be calculated. ALL
means that both of them must be calculated.

cutoff:

if it is an integer, only paths less than or equal to this

length are considered, effectively resulting in an
estimation of the closeness for the given vertices
(which is always an underestimation of the real
closeness, since some vertex pairs will appear as
disconnected even though they are connected).. If
None, the exact closeness is returned.

weights:

edge weights to be used. Can be a sequence or iterable

or even an edge attribute name.

normalized: Whether to normalize the raw closeness scores by

multiplying by the number of vertices minus one.
Return Value
the calculated closenesses in a list

139

Class GraphBase

Package igraph

clusters(mode=STRONG)
Calculates the (strong or weak) clusters for a given graph.
Parameters
mode: must be either STRONG or WEAK, depending on the clusters
being sought. Optional, defaults to STRONG.
Return Value
the component index for every node in the graph.
Attention: this function has a more convenient interface in class Graph which
wraps the result in a VertexClustering object. It is advised to use that.
cocitation(vertices=None)
Calculates cocitation scores for given vertices in a graph.
Parameters
vertices: the vertices to be analysed. If None, all vertices will be
considered.
Return Value
cocitation scores for all given vertices in a matrix.
cohesive_blocks()
Calculates the cohesive block structure of the graph.
Attention: this function has a more convenient interface in class Graph which
wraps the result in a CohesiveBlocks object. It is advised to use that.

140

Class GraphBase

Package igraph

community_edge_betweenness(directed =True, weights=None)

Community structure detection based on the betweenness of the edges in the
network. This algorithm was invented by M Girvan and MEJ Newman, see: M
Girvan and MEJ Newman: Community structure in social and biological
networks, Proc. Nat. Acad. Sci. USA 99, 7821-7826 (2002).
The idea is that the betweenness of the edges connecting two communities is
typically high. So we gradually remove the edge with the highest betweenness
from the network and recalculate edge betweenness after every removal, as
long as all edges are removed.
Parameters
directed: whether to take into account the directedness of the
edges when we calculate the betweenness values.
weights: name of an edge attribute or a list containing edge
weights.
Return Value
a tuple with the merge matrix that describes the dendrogram and
the modularity scores before each merge. The modularity scores use
the weights if the original graph was weighted.
Attention: this function is wrapped in a more convenient syntax in the
derived class Graph. It is advised to use that instead of this version.

141

Class GraphBase

Package igraph

community_fastgreedy(weights=None)
Finds the community structure of the graph according to the algorithm of
Clauset et al based on the greedy optimization of modularity.
This is a bottom-up algorithm: initially every vertex belongs to a separate
community, and communities are merged one by one. In every step, the two
communities being merged are the ones which result in the maximal increase
in modularity.
Parameters
weights: name of an edge attribute or a list containing edge weights
Return Value
a tuple with the following elements:
1. The list of merges
2. The modularity scores before each merge
Attention: this function is wrapped in a more convenient syntax in the
derived class Graph. It is advised to use that instead of this version.
Reference: A. Clauset, M. E. J. Newman and C. Moore: Finding community
structure in very large networks. Phys Rev E 70, 066111 (2004).
See Also: modularity()

142

Class GraphBase

Package igraph

community_infomap(edge_weights=None, vertex_weights=None,
trials=10)
Finds the community structure of the network according to the Infomap
method of Martin Rosvall and Carl T. Bergstrom.
See http://www.mapequation.org for a visualization of the algorithm or one of
the references provided below.
Parameters
edge_weights:

name of an edge attribute or a list containing

edge weights.

vertex_weights: name of an vertex attribute or a list containing

vertex weights.
trials:

the number of attempts to partition the network.

Return Value
the calculated membership vector and the corresponding codelength
in a tuple.
Reference:
M. Rosvall and C. T. Bergstrom: Maps of information flow
reveal community structure in complex networks. PNAS 105,
1118 (2008). http://arxiv.org/abs/0707.0609
M. Rosvall, D. Axelsson and C. T. Bergstrom: The map
equation. Eur Phys J Special Topics 178, 13 (2009).
http://arxiv.org/abs/0906.1405

143

Class GraphBase

Package igraph

community_label_propagation(weights=None, initial =None, fixed =None)

Finds the community structure of the graph according to the label
propagation method of Raghavan et al.
Initially, each vertex is assigned a different label. After that, each vertex
chooses the dominant label in its neighbourhood in each iteration. Ties are
broken randomly and the order in which the vertices are updated is
randomized before every iteration. The algorithm ends when vertices reach a
consensus.
Note that since ties are broken randomly, there is no guarantee that the
algorithm returns the same community structure after each run. In fact, they
frequently differ. See the paper of Raghavan et al on how to come up with an
aggregated community structure.
Parameters
weights: name of an edge attribute or a list containing edge weights
initial: name of a vertex attribute or a list containing the initial
vertex labels. Labels are identified by integers from zero
to n-1 where n is the number of vertices. Negative
numbers may also be present in this vector, they represent
unlabeled vertices.
fixed:

a list of booleans for each vertex. True corresponds to

vertices whose labeling should not change during the
algorithm. It only makes sense if initial labels are also
given. Unlabeled vertices cannot be fixed. Note that
vertex attribute names are not accepted here.

Return Value
the resulting membership vector
Reference: Raghavan, U.N. and Albert, R. and Kumara, S. Near linear time
algorithm to detect community structures in large-scale networks. Phys Rev E
76:036106, 2007. http://arxiv.org/abs/0709.2938 .

144

Class GraphBase

Package igraph

community_leading_eigenvector(n=-1, arpack_options=None,
weights=None)
A proper implementation of Newmans eigenvector community structure
detection. Each split is done by maximizing the modularity regarding the
original network. See the reference for details.
Parameters
n:

the desired number of communities. If negative,

the algorithm tries to do as many splits as
possible. Note that the algorithm wont split a
community further if the signs of the leading
eigenvector are all the same.

arpack_options: an ARPACKOptions object used to fine-tune the

ARPACK eigenvector calculation. If omitted, the
module-level variable called arpack_options is
used.
weights:

name of an edge attribute or a list containing

edge weights

Return Value
a tuple where the first element is the membership vector of the
clustering and the second element is the merge matrix.
Attention: this function is wrapped in a more convenient syntax in the
derived class Graph. It is advised to use that instead of this version.
Reference: MEJ Newman: Finding community structure in networks using
the eigenvectors of matrices, arXiv:physics/0605087

145

Class GraphBase

Package igraph

community_multilevel(weights=None, return_levels=True)
Finds the community structure of the graph according to the multilevel
algorithm of Blondel et al. This is a bottom-up algorithm: initially every
vertex belongs to a separate community, and vertices are moved between
communities iteratively in a way that maximizes the vertices local
contribution to the overall modularity score. When a consensus is reached (i.e.
no single move would increase the modularity score), every community in the
original graph is shrank to a single vertex (while keeping the total weight of
the incident edges) and the process continues on the next level. The algorithm
stops when it is not possible to increase the modularity any more after
shrinking the communities to vertices.
Parameters
weights:

name of an edge attribute or a list containing edge

weights

return_levels: if True, returns the multilevel result. If False,

only the best level (corresponding to the best
modularity) is returned.
Return Value
either a single list describing the community membership of each
vertex (if return_levels is False), or a list of community
membership vectors, one corresponding to each level and a list of
corresponding modularities (if return_levels is True).
Attention: this function is wrapped in a more convenient syntax in the
derived class Graph. It is advised to use that instead of this version.
Reference: VD Blondel, J-L Guillaume, R Lambiotte and E Lefebvre: Fast
unfolding of community hierarchies in large networks. J Stat Mech P10008
(2008), http://arxiv.org/abs/0803.0476
See Also: modularity()

146

Class GraphBase

Package igraph

community_optimal_modularity(weights=None)
Calculates the optimal modularity score of the graph and the corresponding
community structure.
This function uses the GNU Linear Programming Kit to solve a large integer
optimization problem in order to find the optimal modularity score and the
corresponding community structure, therefore it is unlikely to work for graphs
larger than a few (less than a hundred) vertices. Consider using one of the
heuristic approaches instead if you have such a large graph.
Parameters
weights: name of an edge attribute or a list containing edge
weights.
Return Value
the calculated membership vector and the corresponding modularity
in a tuple.

147

Class GraphBase

Package igraph

community_spinglass(weights=None, spins=25, parupdate=False,

start_temp=1, stop_temp=0.01, cool_fact=0.99, update_rule="config",
gamma=1, implementation="orig", lambda=1)
Finds the community structure of the graph according to the spinglass
community detection method of Reichardt & Bornholdt.
Parameters
weights:

edge weights to be used. Can be a sequence or

iterable or even an edge attribute name.

spins:

integer, the number of spins to use. This is the

upper limit for the number of communities. It is
not a problem to supply a (reasonably) big
number here, in which case some spin states will
be unpopulated.

parupdate:

whether to update the spins of the vertices in

parallel (synchronously) or not

start_temp:

the starting temperature

stop_temp:

the stop temperature

cool_fact:

cooling factor for the simulated annealing

update_rule:

specifies the null model of the simulation.

Possible values are "config" (a random graph
with the same vertex degrees as the input graph)
or "simple" (a random graph with the same
number of edges)

gamma:

the gamma argument of the algorithm, specifying

the balance between the importance of present
and missing edges within a community. The
default value of 1.0 assigns equal importance to
both of them.

implementation: currently igraph contains two implementations for

the lambda argument of the algorithm, which

specifies the balance between the importance of
present and missing negatively weighted edges
within a community. Smaller values of lambda
lead to communities with less negative
intra-connectivity. If the argument is zero, the
algorithm reduces to a graph coloring algorithm,
using the number
of spins as colors. This
148
argument is ignored if the original
implementation is used.

Return Value
the community membership vector.

Class GraphBase

Package igraph

community_walktrap(weights=None, steps=None)
Finds the community structure of the graph according to the random walk
method of Latapy & Pons.
The basic idea of the algorithm is that short random walks tend to stay in the
same community. The method provides a dendrogram.
Parameters
weights: name of an edge attribute or a list containing edge weights
Return Value
a tuple with the list of merges and the modularity scores
corresponding to each merge
Attention: this function is wrapped in a more convenient syntax in the
derived class Graph. It is advised to use that instead of this version.
Reference: Pascal Pons, Matthieu Latapy: Computing communities in large
networks using random walks, http://arxiv.org/abs/physics/0512106 .
See Also: modularity()
complementer(loops=False)
Returns the complementer of the graph
Parameters
loops: whether to include loop edges in the complementer.
Return Value
the complementer of the graph
compose(other )
Returns the composition of two graphs.

149

Class GraphBase

Package igraph

constraint(vertices=None, weights=None)
Calculates Burts constraint scores for given vertices in a graph.
Burts constraint is higher if ego has less, or mutually stronger related (i.e.
more redundant) contacts. Burts measure of constraint, C[i], of vertex is ego
network V[i], is defined for directed and valued graphs as follows:
C[i] = sum( sum( (p[i,q] p[q,j])^2, q in V[i], q != i,j ), j in V[], j != i)
for a graph of order (ie. number od vertices) N, where proportional tie
strengths are defined as follows:
p[i,j]=(a[i,j]+a[j,i]) / sum(a[i,k]+a[k,i], k in V[i], k != i), a[i,j] are elements of
A and the latter being the graph adjacency matrix.
For isolated vertices, constraint is undefined.
Parameters
vertices: the vertices to be analysed or None for all vertices.
weights: weights associated to the edges. Can be an attribute
name as well. If None, every edge will have the same
weight.
Return Value
constraint scores for all given vertices in a matrix.

150

Class GraphBase

Package igraph

contract_vertices(mapping, combine_attrs=None)
Contracts some vertices in the graph, i.e. replaces groups of vertices with
single vertices. Edges are not affected.
Parameters
mapping:

numeric vector which gives the mapping between

old and new vertex IDs. Vertices having the same
new vertex ID in this vector will be remapped into
a single new vertex. It is safe to pass the
membership vector of a VertexClustering object
here.

combine_attrs: specifies how to combine the attributes of the

vertices being collapsed into a single one. If it is
None, all the attributes will be lost. If it is a
function, the attributes of the vertices will be
collected and passed on to that function which will
return the new attribute value that has to be
assigned to the single collapsed vertex. It can also
be one of the following string constants which
define built-in collapsing functions: sum, prod,
mean, median, max, min, first, last, random. You
can also specify different combination functions for
different attributes by passing a dict here which
maps attribute names to functions. See
Graph.simplify() for more details.
Return Value
None.
See Also: Graph.simplify()
convergence_degree()
Undocumented (yet).
convergence_field_size()
Undocumented (yet).
copy()
Creates an exact deep copy of the graph.

151

Class GraphBase

Package igraph

coreness(mode=ALL)
Finds the coreness (shell index) of the vertices of the network.
The k -core of a graph is a maximal subgraph in which each vertex has at least
degree k. (Degree here means the degree in the subgraph of course). The
coreness of a vertex is k if it is a member of the k -core but not a member of
the k+1 -core.
Parameters
mode: whether to compute the in-corenesses (IN), the out-corenesses
(OUT) or the undirected corenesses (ALL). Ignored and
assumed to be ALL for undirected graphs.
Return Value
the corenesses for each vertex.
Reference: Vladimir Batagelj, Matjaz Zaversnik: An O(m) Algorithm for
Core Decomposition of Networks.

152

Class GraphBase

Package igraph

count_isomorphisms_vf2(other =None, color1 =None, color2 =None,

edge_color1 =None, edge_color2 =None, node_compat_fn=None,
edge_compat_fn=None)
Determines the number of isomorphisms between the graph and another one
Vertex and edge colors may be used to restrict the isomorphisms, as only
vertices and edges with the same color will be allowed to match each other.
Parameters
other:

the other graph. If None, the number of

automorphisms will be returned.

color1:

optional vector storing the coloring of the vertices

of the first graph. If None, all vertices have the
same color.

color2:

optional vector storing the coloring of the vertices

of the second graph. If None, all vertices have the
same color.

edge_color1:

optional vector storing the coloring of the edges of

the first graph. If None, all edges have the same
color.

edge_color2:

optional vector storing the coloring of the edges of

the second graph. If None, all edges have the
same color.

node_compat_fn: a function that receives the two graphs and two

node indices (one from the first graph, one from
the second graph) and returns True if the nodes
given by the two indices are compatible (i.e. they
could be matched to each other) or False
otherwise. This can be used to restrict the set of
isomorphisms based on node-specific criteria that
are too complicated to be represented by node
color vectors (i.e. the color1 and color2
parameters). None means that every node is
compatible with every other node.
edge_compat_fn: a function that receives the two graphs and two
edge indices (one from the first graph, one from
the second graph) and returns True if the edges
given by the two indices are compatible (i.e. they
could be matched to each other) or False
otherwise. This can be used to restrict the set of
isomorphisms based on edge-specific criteria that
are too complicated to be represented by edge
color vectors (i.e. the edge_color1 and
edge_color2 parameters). None means that
153
every edge is compatible
with every other node.
Return Value
the number of isomorphisms between the two given graphs (or the
number of automorphisms if other is None.

Class GraphBase

Package igraph

count_multiple(edges=None)
Counts the multiplicities of the given edges.
Parameters
edges: edge indices for which we want to count their multiplicity. If
None, all edges are counted.
Return Value
the multiplicities of the given edges as a list.

154

Class GraphBase

Package igraph

count_subisomorphisms_vf2(other, color1 =None, color2 =None,

edge_color1 =None, edge_color2 =None, node_compat_fn=None,
edge_compat_fn=None)
Determines the number of subisomorphisms between the graph and another
one
Vertex and edge colors may be used to restrict the isomorphisms, as only
vertices and edges with the same color will be allowed to match each other.
Parameters
other:

the other graph.

color1:

optional vector storing the coloring of the vertices

of the first graph. If None, all vertices have the
same color.

color2:

optional vector storing the coloring of the vertices

of the second graph. If None, all vertices have the
same color.

edge_color1:

optional vector storing the coloring of the edges of

the first graph. If None, all edges have the same
color.

edge_color2:

optional vector storing the coloring of the edges of

the second graph. If None, all edges have the
same color.

node_compat_fn: a function that receives the two graphs and two

node indices (one from the first graph, one from
the second graph) and returns True if the nodes
given by the two indices are compatible (i.e. they
could be matched to each other) or False
otherwise. This can be used to restrict the set of
isomorphisms based on node-specific criteria that
are too complicated to be represented by node
color vectors (i.e. the color1 and color2
parameters). None means that every node is
compatible with every other node.
edge_compat_fn: a function that receives the two graphs and two
edge indices (one from the first graph, one from
the second graph) and returns True if the edges
given by the two indices are compatible (i.e. they
could be matched to each other) or False
otherwise. This can be used to restrict the set of
isomorphisms based on edge-specific criteria that
are too complicated to be represented by edge
color vectors (i.e. the edge_color1 and
edge_color2 parameters). None means that
155
every edge is compatible
with every other node.
Return Value
the number of subisomorphisms between the two given graphs

Class GraphBase

Package igraph

decompose(mode=STRONG, maxcompno=None, minelements=1)

Decomposes the graph into subgraphs.
Parameters
mode:

must be either STRONG or WEAK, depending on

the clusters being sought.

maxcompno:

maximum number of components to return. None

means all possible components.

minelements: minimum number of vertices in a component. By

setting this to 2, isolated vertices are not returned as
separate components.
Return Value
a list of the subgraphs. Every returned subgraph is a copy of the
original.
degree(vertices, mode=ALL, loops=True)
Returns some vertex degrees from the graph.
This method accepts a single vertex ID or a list of vertex IDs as a parameter,
and returns the degree of the given vertices (in the form of a single integer or a
list, depending on the input parameter).
Parameters
vertices: a single vertex ID or a list of vertex IDs
mode:

the type of degree to be returned (OUT for out-degrees,

IN IN for in-degrees or ALL for the sum of them).

loops:

whether self-loops should be counted.

delete_edges(es)
Removes edges from the graph.
All vertices will be kept, even if they lose all their edges. Nonexistent edges
will be silently ignored.
Parameters
es: the list of edges to be removed. Edges are identifed by edge IDs.
EdgeSeq objects are also accepted here.
delete_vertices(vs)
Deletes vertices and all its edges from the graph.
Parameters
vs: a single vertex ID or the list of vertex IDs to be deleted.
156

Class GraphBase

Package igraph

density(loops=False)
Calculates the density of the graph.
Parameters
loops: whether to take loops into consideration. If True, the
algorithm assumes that there might be some loops in the
graph and calculates the density accordingly. If False, the
algorithm assumes that there cant be any loops.
Return Value
the reciprocity of the graph.
diameter(directed =True, unconn=True, weights=None)
Calculates the diameter of the graph.
Parameters
directed: whether to consider directed paths.
unconn:

if True and the graph is unconnected, the longest

geodesic within a component will be returned. If False
and the graph is unconnected, the result is the number of
vertices if there are no weights or infinity if there are
weights.

weights: edge weights to be used. Can be a sequence or iterable or

even an edge attribute name.
Return Value
the diameter
difference(other )
Subtracts the given graph from the original
disjoint_union(graphs)
Creates the disjoint union of two (or more) graphs.
Parameters
graphs: the list of graphs to be united with the current one.

157

Class GraphBase

Package igraph

diversity(vertices=None, weights=None)
Calculates the structural diversity index of the vertices.
The structural diversity index of a vertex is simply the (normalized) Shannon
entropy of the weights of the edges incident on the vertex.
The measure is defined for undirected graphs only; edge directions are ignored.
Parameters
vertices: the vertices for which the diversity indices must be
returned. If None, uses all of the vertices in the graph.
weights: edge weights to be used. Can be a sequence or iterable or
even an edge attribute name.
Return Value
the calculated diversity indices in a list, or a single number if a single
vertex was supplied.
Reference: Eagle N, Macy M and Claxton R: Network diversity and
economic development, Science 328, 10291031, 2010.
dyad_census()
Dyad census, as defined by Holland and Leinhardt
Dyad census means classifying each pair of vertices of a directed graph into
three categories: mutual, there is an edge from a to b and also from b to a;
asymmetric, there is an edge either from a to b or from b to a but not the
other way and null, no edges between a and b.
Return Value
the number of mutual, asymmetric and null connections in a 3-tuple.
Attention: this function has a more convenient interface in class Graph which
wraps the result in a DyadCensus object. It is advised to use that.

158

Class GraphBase

Package igraph

eccentricity(vertices=None, mode=ALL)
Calculates the eccentricities of given vertices in a graph.
The eccentricity of a vertex is calculated by measuring the shortest distance
from (or to) the vertex, to (or from) all other vertices in the graph, and taking
the maximum.
Parameters
vertices: the vertices for which the eccentricity scores must be
returned. If None, uses all of the vertices in the graph.
mode:

must be one of IN, OUT and ALL. IN means that edge

directions are followed; OUT means that edge directions
are followed the opposite direction; ALL means that
directions are ignored. The argument has no effect for
undirected graphs.

Return Value
the calculated eccentricities in a list, or a single number if a single
vertex was supplied.
ecount()
Counts the number of edges.
Return Value
the number of edges in the graph.
(type=integer)
edge_attributes()
Return Value
the attribute name list of the graphs edges

159

Class GraphBase

Package igraph

edge_betweenness(directed =True, cutoff =None, weights=None)

Calculates or estimates the edge betweennesses in a graph.
Parameters
directed: whether to consider directed paths.
cutoff:

if it is an integer, only paths less than or equal to this

length are considered, effectively resulting in an
estimation of the betweenness values. If None, the exact
betweennesses are returned.

weights: edge weights to be used. Can be a sequence or iterable or

even an edge attribute name.
Return Value
a list with the (exact or estimated) edge betweennesses of all edges.
edge_connectivity(source=-1, target=-1, checks=True)
Calculates the edge connectivity of the graph or between some vertices.
The edge connectivity between two given vertices is the number of edges that
have to be removed in order to disconnect the two vertices into two separate
components. This is also the number of edge disjoint directed paths between
the vertices. The edge connectivity of the graph is the minimal edge
connectivity over all vertex pairs.
This method calculates the edge connectivity of a given vertex pair if both the
source and target vertices are given. If none of them is given (or they are both
negative), the overall edge connectivity is returned.
Parameters
source: the source vertex involved in the calculation.
target: the target vertex involved in the calculation.
checks: if the whole graph connectivity is calculated and this is
True, igraph performs some basic checks before calculation.
If the graph is not strongly connected, then the
connectivity is obviously zero. If the minimum degree is
one, then the connectivity is also one. These simple checks
are much faster than checking the entire graph, therefore it
is advised to set this to True. The parameter is ignored if
the connectivity between two given vertices is computed.
Return Value
the edge connectivity

160

Class GraphBase

Package igraph

eigenvector_centrality(directed =True, scale=True, weights=None,

return_eigenvalue=False, arpack_options=None)
Calculates the eigenvector centralities of the vertices in a graph.
Parameters
directed:

whether to consider edge directions in a

directed graph. Ignored for undirected graphs.

scale:

whether to normalize the centralities so the

largest one will always be 1.

weights:

edge weights given as a list or an edge

attribute. If None, all edges have equal weight.

return_eigenvalue: whether to return the actual largest

eigenvalue along with the centralities
arpack_options:

an ARPACKOptions object that can be used to

fine-tune the calculation. If it is omitted, the
module-level variable called arpack_options
is used.

Return Value
the eigenvector centralities in a list and optionally the largest
eigenvalue (as a second member of a tuple)
farthest_points(directed =True, unconn=True, weights=None)
Returns two vertex IDs whose distance equals the actual diameter of the graph.
If there are many shortest paths with the length of the diameter, it returns the
first one it found.
Parameters
directed: whether to consider directed paths.
unconn:

if True and the graph is unconnected, the longest

geodesic within a component will be returned. If False
and the graph is unconnected, the result contains the
number of vertices if there are no weights or infinity if
there are weights.

weights: edge weights to be used. Can be a sequence or iterable or

even an edge attribute name.
Return Value
a triplet containing the two vertex IDs and their distance. The IDs
are None if the graph is unconnected and unconn is False.

161

Class GraphBase

Package igraph

feedback_arc_set(weights=None, method ="eades")

Calculates an approximately or exactly minimal feedback arc set.
A feedback arc set is a set of edges whose removal makes the graph acyclic.
Since this is always possible by removing all the edges, we are in general
interested in removing the smallest possible number of edges, or an edge set
with as small total weight as possible. This method calculates one such edge
set. Note that the task is trivial for an undirected graph as it is enough to find
a spanning tree and then remove all the edges not in the spanning tree. Of
course it is more complicated for directed graphs.
Parameters
weights: edge weights to be used. Can be a sequence or iterable or
even an edge attribute name. When given, the algorithm
will strive to remove lightweight edges in order to
minimize the total weight of the feedback arc set.
method: the algorithm to use. "eades" uses the greedy cycle
breaking heuristic of Eades, Lin and Smyth, which is
linear in the number of edges but not necessarily optimal;
however, it guarantees that the number of edges to be
removed is smaller than |E|/2 - |V|/6. "ip" uses an
integer programming formulation which is guaranteed to
yield an optimal result, but is too slow for large graphs.
Return Value
the IDs of the edges to be removed, in a list.
Reference: Eades P, Lin X and Smyth WF: A fast and effective heuristic for
the feedback arc set problem. In: Proc Inf Process Lett 319-323, 1993.
get_adjacency(type=GET_ADJACENCY_BOTH, eids=False)
Returns the adjacency matrix of a graph.
Parameters
type: either GET_ADJACENCY_LOWER (uses the lower triangle of the
matrix) or GET_ADJACENCY_UPPER (uses the upper triangle) or
GET_ADJACENCY_BOTH (uses both parts). Ignored for directed
graphs.
eids: if True, the result matrix will contain zeros for non-edges and
the ID of the edge plus one for edges in the appropriate cell.
If False, the result matrix will contain the number of edges
for each vertex pair.
Return Value
the adjacency matrix.

162

Class GraphBase

Package igraph

get_all_shortest_paths(v, to=None, mode=OUT)

Calculates all of the shortest paths from/to a given node in a graph.
Parameters
v:
the source/destination for the calculated paths
to:

a vertex selector describing the destination/source for the

calculated paths. This can be a single vertex ID, a list of
vertex IDs, a single vertex name, a list of vertex names or a
VertexSeq object. None means all the vertices.

mode: the directionality of the paths. IN means to calculate

incoming paths, OUT means to calculate outgoing paths, ALL
means to calculate both ones.
Return Value
all of the shortest path from the given node to every other reachable
node in the graph in a list. Note that in case of mode=IN, the
vertices in a path are returned in reversed order!
get_diameter(directed =True, unconn=True, weights=None)
Returns a path with the actual diameter of the graph.
If there are many shortest paths with the length of the diameter, it returns the
first one it founds.
Parameters
directed: whether to consider directed paths.
unconn:

if True and the graph is unconnected, the longest

geodesic within a component will be returned. If False
and the graph is unconnected, the result is the number of
vertices if there are no weights or infinity if there are
weights.

weights: edge weights to be used. Can be a sequence or iterable or

even an edge attribute name.
Return Value
the vertices in the path in order.
get_edgelist()
Returns the edge list of a graph.

163

Class GraphBase

Package igraph

get_eid(v1, v2, directed =True, error =True)

Returns the edge ID of an arbitrary edge between vertices v1 and v2
Parameters
v1:
v2:

the first vertex ID

the second vertex ID

directed: whether edge directions should be considered in directed

graphs. The default is True. Ignored for undirected
graphs.
error:

if True, an exception will be raised when the given edge

does not exist. If False, -1 will be returned in that case.

Return Value
the edge ID of an arbitrary edge between vertices v1 and v2
get_eids(pairs=None, path=None, directed =True, error =True)
Returns the edge IDs of some edges between some vertices.
This method can operate in two different modes, depending on which of the
keyword arguments pairs and path are given.
The method does not consider multiple edges; if there are multiple edges
between a pair of vertices, only the ID of one of the edges is returned.
Parameters
pairs:

path:

a list of integer pairs. Each integer pair is considered as a

source-target vertex pair; the corresponding edge is
looked up in the graph and the edge ID is returned for
each pair.
a list of vertex IDs. The list is considered as a continuous
path from the first vertex to the last, passing through
the intermediate vertices. The corresponding edge IDs
between the first and the second, the second and the
third and so on are looked up in the graph and the edge
IDs are returned. If both path and pairs are given, the
two lists are concatenated.

directed: whether edge directions should be considered in directed

graphs. The default is True. Ignored for undirected
graphs.
error:

if True, an exception will be raised if a given edge does

not exist. If False, -1 will be returned in that case.

Return Value
the edge IDs in a list
164

Class GraphBase

Package igraph

get_incidence(types)
Internal function, undocumented.
See Also: Graph.get_incidence()

165

Class GraphBase

Package igraph

get_isomorphisms_vf2(other =None, color1 =None, color2 =None,

edge_color1 =None, edge_color2 =None, node_compat_fn=None,
edge_compat_fn=None)
Returns all isomorphisms between the graph and another one
Vertex and edge colors may be used to restrict the isomorphisms, as only
vertices and edges with the same color will be allowed to match each other.
Parameters
other:

the other graph. If None, the automorphisms will

be returned.

color1:

optional vector storing the coloring of the vertices

of the first graph. If None, all vertices have the
same color.

color2:

optional vector storing the coloring of the vertices

of the second graph. If None, all vertices have the
same color.

edge_color1:

optional vector storing the coloring of the edges of

the first graph. If None, all edges have the same
color.

edge_color2:

optional vector storing the coloring of the edges of

the second graph. If None, all edges have the
same color.

node_compat_fn: a function that receives the two graphs and two

node indices (one from the first graph, one from
the second graph) and returns True if the nodes
given by the two indices are compatible (i.e. they
could be matched to each other) or False
otherwise. This can be used to restrict the set of
isomorphisms based on node-specific criteria that
are too complicated to be represented by node
color vectors (i.e. the color1 and color2
parameters). None means that every node is
compatible with every other node.
edge_compat_fn: a function that receives the two graphs and two
edge indices (one from the first graph, one from
the second graph) and returns True if the edges
given by the two indices are compatible (i.e. they
could be matched to each other) or False
otherwise. This can be used to restrict the set of
isomorphisms based on edge-specific criteria that
are too complicated to be represented by edge
color vectors (i.e. the edge_color1 and
edge_color2 parameters). None means that
166
every edge is compatible
with every other node.
Return Value
a list of lists, each item of the list containing the mapping from
vertices of the second graph to the vertices of the first one

Class GraphBase

Package igraph

get_shortest_paths(v, to=None, weights=None, mode=OUT,

output="vpath")
Calculates the shortest paths from/to a given node in a graph.
Parameters
v:
to:

the source/destination for the calculated paths

a vertex selector describing the destination/source for the
calculated paths. This can be a single vertex ID, a list of
vertex IDs, a single vertex name, a list of vertex names or
a VertexSeq object. None means all the vertices.

weights: edge weights in a list or the name of an edge attribute

holding edge weights. If None, all edges are assumed to
have equal weight.
mode:

the directionality of the paths. IN means to calculate

incoming paths, OUT means to calculate outgoing paths,
ALL means to calculate both ones.

output: determines what should be returned. If this is "vpath", a

list of vertex IDs will be returned, one path for each
target vertex. For unconnected graphs, some of the list
elements may be empty. Note that in case of mode=IN,
the vertices in a path are returned in reversed order. If
output="epath", edge IDs are returned instead of vertex
IDs.
Return Value
see the documentation of the output parameter.

167

Class GraphBase

Package igraph

get_subisomorphisms_lad(other, domains=None, induced =False,

time_limit=0)
Returns all subisomorphisms between the graph and another one using the
LAD algorithm.
The optional domains argument may be used to restrict vertices that may
match each other. You can also specify whether you are interested in induced
subgraphs only or not.
Parameters
other:

the pattern graph we are looking for in the graph.

domains:

a list of lists, one sublist belonging to each vertex in

the template graph. Sublist i contains the indices of
the vertices in the original graph that may match
vertex i in the template graph. None means that every
vertex may match every other vertex.

induced:

whether to consider induced subgraphs only.

time_limit: an optimal time limit in seconds. Only the integral

part of this number is taken into account. If the time
limit is exceeded, the method will throw an exception.
Return Value
a list of lists, each item of the list containing the mapping from
vertices of the second graph to the vertices of the first one

168

Class GraphBase

Package igraph

get_subisomorphisms_vf2(other, color1 =None, color2 =None,

edge_color1 =None, edge_color2 =None, node_compat_fn=None,
edge_compat_fn=None)
Returns all subisomorphisms between the graph and another one
Vertex and edge colors may be used to restrict the isomorphisms, as only
vertices and edges with the same color will be allowed to match each other.
Parameters
other:

the other graph.

color1:

optional vector storing the coloring of the vertices

of the first graph. If None, all vertices have the
same color.

color2:

optional vector storing the coloring of the vertices

of the second graph. If None, all vertices have the
same color.

edge_color1:

optional vector storing the coloring of the edges of

the first graph. If None, all edges have the same
color.

edge_color2:

optional vector storing the coloring of the edges of

the second graph. If None, all edges have the
same color.

node_compat_fn: a function that receives the two graphs and two

node indices (one from the first graph, one from
the second graph) and returns True if the nodes
given by the two indices are compatible (i.e. they
could be matched to each other) or False
otherwise. This can be used to restrict the set of
isomorphisms based on node-specific criteria that
are too complicated to be represented by node
color vectors (i.e. the color1 and color2
parameters). None means that every node is
compatible with every other node.
edge_compat_fn: a function that receives the two graphs and two
edge indices (one from the first graph, one from
the second graph) and returns True if the edges
given by the two indices are compatible (i.e. they
could be matched to each other) or False
otherwise. This can be used to restrict the set of
isomorphisms based on edge-specific criteria that
are too complicated to be represented by edge
color vectors (i.e. the edge_color1 and
edge_color2 parameters). None means that
every edge is compatible with every other node.
169

Return Value
a list of lists, each item of the list containing the mapping from
vertices of the second graph to the vertices of the first one

Class GraphBase

Package igraph

girth(return_shortest_circle=False)
Returns the girth of the graph.
The girth of a graph is the length of the shortest circle in it.
Parameters
return_shortest_circle: whether to return one of the shortest
circles found in the graph.
Return Value
the length of the shortest circle or (if return_shortest_circle) is
true, the shortest circle itself as a list
gomory_hu_tree(capacity=None)
Internal function, undocumented.
See Also: Graph.gomory_hu_tree()
has_multiple()
Checks whether the graph has multiple edges.
Return Value
True if the graph has at least one multiple edge, False otherwise.
(type=boolean)

170

Class GraphBase

Package igraph

hub_score(weights=None, scale=True, arpack_options=None,

return_eigenvalue=False)
Calculates Kleinbergs hub score for the vertices of the graph
Parameters
weights:

edge weights to be used. Can be a sequence or

iterable or even an edge attribute name.

scale:

whether to normalize the scores so that the

largest one is 1.

arpack_options:

an ARPACKOptions object used to fine-tune

the ARPACK eigenvector calculation. If
omitted, the module-level variable called
arpack_options is used.

return_eigenvalue: whether to return the largest eigenvalue

Return Value
the hub scores in a list and optionally the largest eigenvalue as a
second member of a tuple
See Also: authority_score()
incident(vertex, mode=OUT)
Returns the edges a given vertex is incident on.
Parameters
vertex: a vertex ID
mode:

whether to return only predecessors (OUT), successors (IN)

or both (ALL). Ignored for undirected graphs.

independence_number()
Returns the independence number of the graph.
The independence number of the graph is the size of the largest independent
vertex set.
See Also: largest_independent_vertex_sets() for the largest independent
vertex sets

171

Class GraphBase

Package igraph

independent_vertex_sets(min=0, max =0)

Returns some or all independent vertex sets of the graph as a list of tuples.
Two vertices are independent if there is no edge between them. Members of an
independent vertex set are mutually independent.
Parameters
min: the minimum size of sets to be returned. If zero or negative, no
lower bound will be used.
max: the maximum size of sets to be returned. If zero or negative,
no upper bound will be used.
induced_subgraph(vertices, implementation="auto")
Returns a subgraph spanned by the given vertices.
Parameters
vertices:

a list containing the vertex IDs which should be

included in the result.

implementation: the implementation to use when constructing the

172

Class GraphBase

Package igraph

is_bipartite(return_types=False)
Decides whether the graph is bipartite or not.
Vertices of a bipartite graph can be partitioned into two groups A and B in a
way that all edges go between the two groups.
Parameters
return_types: if False, the method will simply return True or
False depending on whether the graph is bipartite
or not. If True, the actual group assignments are
also returned as a list of boolean values. (Note that
the group assignment is not unique, especially if the
graph consists of multiple components, since the
assignments of components are independent from
each other).
Return Value
True if the graph is bipartite, False if not. If return_types is True,
the group assignment is also returned.
is_connected(mode=STRONG)
Decides whether the graph is connected.
Parameters
mode: whether we should calculate strong or weak connectivity.
Return Value
True if the graph is connected, False otherwise.
is_dag()
Checks whether the graph is a DAG (directed acyclic graph).
A DAG is a directed graph with no directed cycles.
Return Value
True if it is a DAG, False otherwise.
(type=boolean)
is_directed()
Checks whether the graph is directed.@return: True if it is directed, False
otherwise.
Return Value
boolean

173

Class GraphBase

Package igraph

is_loop(edges=None)
Checks whether a specific set of edges contain loop edges
Parameters
edges: edge indices which we want to check. If None, all edges are
checked.
Return Value
a list of booleans, one for every edge given
is_minimal_separator(vertices)
Decides whether the given vertex set is a minimal separator.
A minimal separator is a set of vertices whose removal disconnects the graph,
while the removal of any subset of the set keeps the graph connected.
Parameters
vertices: a single vertex ID or a list of vertex IDs
Return Value
True is the given vertex set is a minimal separator, False otherwise.
is_multiple(edges=None)
Checks whether an edge is a multiple edge.
Also works for a set of edges in this case, every edge is checked one by one.
Note that if there are multiple edges going between a pair of vertices, there is
always one of them that is not reported as multiple (only the others). This
allows one to easily detect the edges that have to be deleted in order to make
the graph free of multiple edges.
Parameters
edges: edge indices which we want to check. If None, all edges are
checked.
Return Value
a list of booleans, one for every edge given

174

Class GraphBase

Package igraph

is_mutual(edges=None)
Checks whether an edge has an opposite pair.
Also works for a set of edges in this case, every edge is checked one by one.
The result will be a list of booleans (or a single boolean if only an edge index
is supplied), every boolean corresponding to an edge in the edge set supplied.
True is returned for a given edge a > b if there exists another edge b > a in
the original graph (not the given edge set!). All edges in an undirected graph
are mutual. In case there are multiple edges between a and b, it is enough to
have at least one edge in either direction to report all edges between them as
mutual, so the multiplicity of edges do not matter.
Parameters
edges: edge indices which we want to check. If None, all edges are
checked.
Return Value
a list of booleans, one for every edge given
is_separator(vertices)
Decides whether the removal of the given vertices disconnects the graph.
Parameters
vertices: a single vertex ID or a list of vertex IDs
Return Value
True is the given vertex set is a separator, False if not.
is_simple()
Checks whether the graph is simple (no loop or multiple edges).
Return Value
True if it is simple, False otherwise.
(type=boolean)

175

Class GraphBase

Package igraph

isoclass(vertices)
Returns the isomorphy class of the graph or its subgraph.
Isomorphy class calculations are implemented only for graphs with 3 or 4
vertices.
Parameters
vertices: a list of vertices if we want to calculate the isomorphy
class for only a subset of vertices. None means to use the
full graph.
Return Value
the isomorphy class of the (sub)graph
isomorphic(other )
Checks whether the graph is isomorphic to another graph.
The algorithm being used is selected using a simple heuristic:
If one graph is directed and the other undirected, an exception is thrown.
If the two graphs does not have the same number of vertices and edges, it
returns with False
If the graphs have three or four vertices, then an O(1) algorithm is used
with precomputed data.
Otherwise if the graphs are directed, then the VF2 isomorphism
algorithm is used (see Graph.isomorphic_vf2).
Otherwise the BLISS isomorphism algorithm is used, see
Graph.isomorphic_bliss.
Return Value
True if the graphs are isomorphic, False otherwise.

176

Class GraphBase

Package igraph

isomorphic_bliss(other, return_mapping_12 =False,

return_mapping_21 =False, sh1 ="fm", sh2 ="fm")
Checks whether the graph is isomorphic to another graph, using the BLISS
isomorphism algorithm.
See http://www.tcs.hut.fi/Software/bliss/index.html for more information
about the BLISS algorithm.
Parameters
other:

the other graph with which we want to

compare the graph.

return_mapping_12: if True, calculates the mapping which maps

the vertices of the first graph to the second.
return_mapping_21: if True, calculates the mapping which maps
the vertices of the second graph to the first.
sh1:

splitting heuristics for the first graph as a

case-insensitive string, with the following
possible values:
"f": first non-singleton cell
"fl": first largest non-singleton cell
"fs": first smallest non-singleton cell
"fm": first maximally non-trivially
connected non-singleton cell
"flm": largest maximally non-trivially
connected non-singleton cell
"fsm": smallest maximally non-trivially
connected non-singleton cell

sh2:

splitting heuristics to be used for the second

graph. Accepted values are as above.

Return Value
if no mapping is calculated, the result is True if the graphs are
isomorphic, False otherwise. If any or both mappings are
calculated, the result is a 3-tuple, the first element being the above
mentioned boolean, the second element being the 1 -> 2 mapping
and the third element being the 2 -> 1 mapping. If the
corresponding mapping was not calculated, None is returned in the
appropriate element of the 3-tuple.

177

Class GraphBase

Package igraph

isomorphic_vf2(other =None, color1 =None, color2 =None,

edge_color1 =None, edge_color2 =None, return_mapping_12 =False,
return_mapping_21 =False, node_compat_fn=None,
edge_compat_fn=None, callback =None)
Checks whether the graph is isomorphic to another graph, using the VF2
isomorphism algorithm.
Vertex and edge colors may be used to restrict the isomorphisms, as only
vertices and edges with the same color will be allowed to match each other.
Parameters
other:

the other graph with which we want to

compare the graph. If None, the
automorphjisms of the graph will be tested.

color1:

optional vector storing the coloring of the

vertices of the first graph. If None, all vertices
have the same color.

color2:

optional vector storing the coloring of the

vertices of the second graph. If None, all
vertices have the same color.

edge_color1:

optional vector storing the coloring of the

edges of the first graph. If None, all edges
have the same color.

edge_color2:

optional vector storing the coloring of the

edges of the second graph. If None, all edges
have the same color.

return_mapping_12: if True, calculates the mapping which maps

the vertices of the first graph to the second.
return_mapping_21: if True, calculates the mapping which maps
the vertices of the second graph to the first.
callback:

if not None, the isomorphism search will not

stop at the first match; it will call this
callback function instead for every
isomorphism found. The callback function
must accept four arguments: the first graph,
the second graph, a mapping from the nodes
of the first graph to the second, and a
mapping from the nodes of the second graph
to the first. The function must return True if
the search should continue or False otherwise.

node_compat_fn:

a function that receives the two graphs and

two node indices (one from the first graph,
one from the second graph) and returns True
if the nodes178
given by the two indices are
compatible (i.e. they could be matched to
each other) or False otherwise. This can be
used to restrict the set of isomorphisms based
on node-specific criteria that are too

Class GraphBase

Package igraph

knn(vids=None, weights=None)
Calculates the average degree of the neighbors for each vertex, and the same
quantity as the function of vertex degree.
Parameters
vids:

the vertices for which the calculation is performed. None

means all vertices.

weights: edge weights to be used. Can be a sequence or iterable or

even an edge attribute name. If this is given, the vertex
strength will be used instead of the vertex degree in the
calculations, but the "ordinary" vertex degree will be used
for the second (degree- dependent) list in the result.
Return Value
two lists in a tuple. The first list contains the average degree of
neighbors for each vertex, the second contains the average degree of
neighbors as a function of vertex degree. The zeroth element of this
list corresponds to vertices of degree 1.
laplacian(weights=None, normalized =False)
Returns the Laplacian matrix of a graph.
The Laplacian matrix is similar to the adjacency matrix, but the edges are
denoted with -1 and the diagonal contains the node degrees.
Normalized Laplacian matrices have 1 or 0 in their diagonals (0 for vertices
with no edges), edges are denoted by 1 / sqrt(d_i * d_j) where d_i is the
degree of node i.
Multiple edges and self-loops are silently ignored. Although it is possible to
calculate the Laplacian matrix of a directed graph, it does not make much
sense.
Parameters
weights:

edge weights to be used. Can be a sequence or iterable

or even an edge attribute name. When edge weights
are used, the degree of a node is considered to be the
weight of its incident edges.

normalized: whether to return the normalized Laplacian matrix.

Return Value
the Laplacian matrix.

179

Class GraphBase

Package igraph

largest_cliques()
Returns the largest cliques of the graph as a list of tuples.
Quite intuitively a clique is considered largest if there is no clique with more
vertices in the whole graph. All largest cliques are maximal (i.e.
nonextendable) but not all maximal cliques are largest.
See Also: clique_number() for the size of the largest cliques or
maximal_cliques() for the maximal cliques
largest_independent_vertex_sets()
Returns the largest independent vertex sets of the graph as a list of tuples.
Quite intuitively an independent vertex set is considered largest if there is no
other set with more vertices in the whole graph. All largest sets are maximal
(i.e. nonextendable) but not all maximal sets are largest.
See Also: independence_number() for the size of the largest independent
vertex sets or maximal_independent_vertex_sets() for the maximal
(nonextendable) independent vertex sets
layout_bipartite(types="type", hgap=1, vgap=1, maxiter =100)
Place the vertices of a bipartite graph in two layers.
The layout is created by placing the vertices in two rows, according to their
types. The positions of the vertices within the rows are then optimized to
minimize the number of edge crossings using the heuristic used by the
Sugiyama layout algorithm.
Parameters
types:

an igraph vector containing the vertex types, or an

attribute name. Anything that evalulates to False
corresponds to vertices of the first kind, everything else to
the second kind.

hgap:

minimum horizontal gap between vertices in the same

layer.

vgap:

vertical gap between the two layers.

maxiter: maximum number of iterations to take in the crossing

reduction step. Increase this if you feel that you are
getting too many edge crossings.
Return Value
the calculated layout.

180

Class GraphBase

Package igraph

181

Class GraphBase

Package igraph

layout_drl(weights=None, fixed =None, seed =None, options=None, dim=2)

if None, uses a random starting layout for the algorithm.

If a matrix (list of lists), uses the given matrix as the
starting position.

fixed:

if a seed is given, you can specify some vertices to be kept

options: if you give a string argument here, you can select from five
default preset parameterisations: default, coarsen for a
coarser layout, coarsest for an even coarser layout,
refine for refining an existing layout and final for
finalizing a layout. If you supply an object that is not a
string, the DrL layout parameters are retrieved from the
respective keys of the object (so it should be a dict or
something else that supports the mapping protocol). The
following keys can be used:
edge_cut: edge cutting is done in the late stages of
the algorithm in order to achieve less dense layouts.
Edges are cut if there is a lot of stress on them (a large
value in the objective function sum). The edge cutting
parameter is a value between 0 and 1 with 0
representing no edge cutting and 1 representing
maximal edge cutting.
init_iterations: number of iterations in the
initialization phase
init_temperature: start temperature during
initialization
init_attraction: attraction during initialization
init_damping_mult: damping multiplier during
initialization
182
liquid_iterations, liquid_temperature,
liquid_attraction, liquid_damping_mult: same
parameters for the liquid phase
expansion_iterations, expansion_temperature,

Class GraphBase

Package igraph

layout_fruchterman_reingold(weights=None, maxiter =500,

edge weights to be used. Can be a sequence or iterable

or even an edge attribute name.

maxiter:

the number of iterations to perform. The default is

500.

maxdelta:

the maximum distance to move a vertex in an

iteration. The default is the number of vertices.

area:

the area of the square on which the vertices will be

placed. The default is the square of the number of
vertices.

coolexp:

the cooling exponent of the simulated annealing. The

default is 1.5.

repulserad: determines the radius at which vertex-vertex repulsion

cancels out attraction of adjacent vertices. The default
is the number of vertices^3.
minx:

if not None, it must be a vector with exactly as many

elements as there are vertices in the graph. Each
element is a minimum constraint on the X value of the
vertex in the layout.

maxx:

similar to minx, but with maximum constraints

miny:

similar to minx, but with the Y coordinates

maxy:

similar to maxx, but with the Y coordinates

minz:

similar to minx, but with the Z coordinates. Use only

for 3D layouts (dim=3).

maxz:

similar to maxx, but with the Z coordinates. Use only

for 3D layouts (dim=3).

seed:

if None, uses a random starting layout for the

algorithm. If a matrix (list of lists), uses the given
matrix as the starting position.

dim:

the desired number of dimensions for the layout.

dim=2 means a 2D 183
layout, dim=3 means a 3D layout.

Return Value
the calculated layout.

Class GraphBase

Package igraph

layout_graphopt(niter =500, node_charge=0.001, node_mass=30,

the number of iterations to perform. Should be a

couple of hundred in general.

node_charge:

the charge of the vertices, used to calculate

electric repulsion.

node_mass:

the mass of the vertices, used for the spring

forces

spring_length:

the length of the springs

spring_constant: the spring constant

max_sa_movement: the maximum amount of movement allowed in a
single step along a single axis.
seed:

a matrix containing a seed layout from which

the algorithm will be started. If None, a random
layout will be used.

Return Value
the calculated layout.

184

Class GraphBase

Package igraph

layout_grid(width=0, height=0, dim=2)

the desired number of dimensions for the layout. dim=2

means a 2D layout, dim=3 means a 3D layout.

Return Value
the calculated layout.

185

Class GraphBase

Package igraph

layout_grid_fruchterman_reingold(maxiter =500, maxdelta=None,

the number of iterations to perform.

maxdelta:

the maximum distance to move a vertex in an

iteration. None means the number of vertices.

area:

the area of the square on which the vertices will be

placed. None means the square of maxdelta.

coolexp:

the cooling exponent of the simulated annealing.

repulserad: determines the radius at which vertex-vertex repulsion

cancels out attraction of adjacent vertices. None means
maxiter*maxdelta.
cellsize:

the size of the grid cells. When calculating the

repulsion forces, only vertices in the same or
neighboring grid cells are taken into account. Defaults
to the fourth root of area.

seed:

if None, uses a random starting layout for the

algorithm. If a matrix (list of lists), uses the given
matrix as the starting position.

Return Value
the calculated layout.

186

Class GraphBase

Package igraph

layout_kamada_kawai(maxiter =1000, sigma=None, initemp=10,

the standard base deviation of the position change

proposals. None means the number of vertices / 4

initemp: initial temperature of the simulated annealing.

coolexp: cooling exponent of the simulated annealing.
kkconst: the Kamada-Kawai vertex attraction constant. None
means the square of the number of vertices.
minx:

if not None, it must be a vector with exactly as many

elements as there are vertices in the graph. Each element
is a minimum constraint on the X value of the vertex in
the layout.

maxx:

similar to minx, but with maximum constraints

miny:

similar to minx, but with the Y coordinates

maxy:

similar to maxx, but with the Y coordinates

minz:

similar to minx, but with the Z coordinates. Use only for

3D layouts (dim=3).

maxz:

similar to maxx, but with the Z coordinates. Use only for

3D layouts (dim=3).

seed:

if None, uses a random starting layout for the algorithm.

If a matrix (list of lists), uses the given matrix as the
starting position.

dim:

the desired number of dimensions for the layout. dim=2

means a 2D layout, dim=3 means a 3D layout.

Return Value
the calculated layout.

187

Class GraphBase

Package igraph

layout_lgl(maxiter =150, maxdelta=-1, area=-1, coolexp=1.5,

repulserad =-1, cellsize=-1, root=None)
Places the vertices on a 2D plane according to the Large Graph Layout.
Parameters
maxiter:

the number of iterations to perform.

maxdelta:

the maximum distance to move a vertex in an

iteration. If negative, defaults to the number of
vertices.

area:

the area of the square on which the vertices will be

placed. If negative, defaults to the number of vertices
squared.

coolexp:

the cooling exponent of the simulated annealing.

repulserad: determines the radius at which vertex-vertex repulsion

cancels out attraction of adjacent vertices. If negative,
defaults to area times the number of vertices.
cellsize:

the size of the grid cells. When calculating the

repulsion forces, only vertices in the same or
neighboring grid cells are taken into account. Defaults
to the fourth root of area.

root:

the root vertex, this is placed first, its neighbors in the

first iteration, second neighbors in the second, etc.
None means that a random vertex will be chosen.

Return Value
the calculated layout.

188

Class GraphBase

Package igraph

layout_mds(dist=None, dim=2, arpack_options=None)

dim:

the distance matrix. It must be symmetric and

arpack_options: an ARPACKOptions object used to fine-tune the

ARPACK eigenvector calculation. If omitted, the
module-level variable called arpack_options is
used.
Return Value
the calculated layout.
Reference: Cox & Cox: Multidimensional Scaling (1994), Chapman and Hall,
London.
layout_random(dim=2)
Places the vertices of the graph randomly.
Parameters
dim: the desired number of dimensions for the layout. dim=2 means
a 2D layout, dim=3 means a 3D layout.
Return Value
the coordinate pairs in a list.

189

Class GraphBase

Package igraph

layout_reingold_tilford(mode="out", root=None, rootlevel =None)

Places the vertices on a 2D plane according to the Reingold-Tilford layout
algorithm.
This is a tree layout. If the given graph is not a tree, a breadth-first search is
executed first to obtain a possible spanning tree.
Parameters
mode:

root:

specifies which edges to consider when builing the tree.

rootlevel: this argument is useful when drawing forests which are

not trees. It specifies the level of the root vertices for
every tree in the forest.
Return Value
the calculated layout.
See Also: layout_reingold_tilford_circular
Reference: EM Reingold, JS Tilford: Tidier Drawings of Trees. IEEE
Transactions on Software Engineering 7:22, 223-228, 1981.

190

Class GraphBase

Package igraph

191

Class GraphBase

Package igraph

maxdegree(vertices=None, mode=ALL, loops=False)

Returns the maximum degree of a vertex set in the graph.
This method accepts a single vertex ID or a list of vertex IDs as a parameter,
and returns the degree of the given vertices (in the form of a single integer or a
list, depending on the input parameter).
Parameters
vertices: a single vertex ID or a list of vertex IDs, or None
meaning all the vertices in the graph.
mode:

the type of degree to be returned (OUT for out-degrees,

IN IN for in-degrees or ALL for the sum of them).

loops:

whether self-loops should be counted.

maxflow(source, target, capacity=None)

Returns the maximum flow between the source and target vertices.
Parameters
source:

the source vertex ID

target:

the target vertex ID

capacity: the capacity of the edges. It must be a list or a valid

attribute name or None. In the latter case, every edge
will have the same capacity.
Return Value
a tuple containing the following: the value of the maximum flow
between the given vertices, the flow value on all the edges, the edge
IDs that are part of the corresponding minimum cut, and the vertex
IDs on one side of the cut. For directed graphs, the flow value vector
gives the flow value on each edge. For undirected graphs, the flow
value is positive if the flow goes from the smaller vertex ID to the
bigger one and negative if the flow goes from the bigger vertex ID to
the smaller.
Attention: this function has a more convenient interface in class Graph which
wraps the result in a Flow object. It is advised to use that.

192

Class GraphBase

Package igraph

maxflow_value(source, target, capacity=None)

Returns the value of the maximum flow between the source and target vertices.
Parameters
source:

the source vertex ID

target:

the target vertex ID

capacity: the capacity of the edges. It must be a list or a valid

attribute name or None. In the latter case, every edge
will have the same capacity.
Return Value
the value of the maximum flow between the given vertices
maximal_cliques(min=0, max =0)
Returns the maximal cliques of the graph as a list of tuples.
A maximal clique is a clique which cant be extended by adding any other
vertex to it. A maximal clique is not necessarily one of the largest cliques in
the graph.
Parameters
min: the minimum size of maximal cliques to be returned. If zero or
negative, no lower bound will be used.
max: the maximum size of maximal cliques to be returned. If zero or
negative, no upper bound will be used. If nonzero, the size of
every maximal clique found will be compared to this value and
a clique will be returned only if its size is smaller than this
limit.
See Also: largest_cliques() for the largest cliques.
maximal_independent_vertex_sets()
Returns the maximal independent vertex sets of the graph as a list of tuples.
A maximal independent vertex set is an independent vertex set which cant be
extended by adding any other vertex to it. A maximal independent vertex set
is not necessarily one of the largest independent vertex sets in the graph.
See Also: largest_independent_vertex_sets() for the largest independent
vertex sets
Reference: S. Tsukiyama, M. Ide, H. Ariyoshi and I. Shirawaka: A new
algorithm for generating all the maximal independent sets. SIAM J
Computing, 6:505517, 1977.

193

Class GraphBase

Package igraph

mincut(source=None, target=None, capacity=None)

Calculates the minimum cut between the source and target vertices or within
the whole graph.
The minimum cut is the minimum set of edges that needs to be removed to
separate the source and the target (if they are given) or to disconnect the
graph (if the source and target are not given). The minimum is calculated
using the weights (capacities) of the edges, so the cut with the minimum total
capacity is calculated. For undirected graphs and no source and target, the
method uses the Stoer-Wagner algorithm. For a given source and target, the
method uses the push-relabel algorithm; see the references below.
Parameters
source:

target:

the source vertex ID. If None, target must also be

{None} and the calculation will be done for the entire
graph (i.e. all possible vertex pairs).
the target vertex ID. If None, source must also be
{None} and the calculation will be done for the entire
graph (i.e. all possible vertex pairs).

capacity: the capacity of the edges. It must be a list or a valid

194

Class GraphBase

Package igraph

mincut_value(source=-1, target=-1, capacity=None)

Returns the minimum cut between the source and target vertices or within the
whole graph.
Parameters
source:

target:

the source vertex ID. If negative, the calculation is done

for every vertex except the target and the minimum is
returned.
the target vertex ID. If negative, the calculation is done
for every vertex except the source and the minimum is
returned.

capacity: the capacity of the edges. It must be a list or a valid

attribute name or None. In the latter case, every edge
will have the same capacity.
Return Value
the value of the minimum cut between the given vertices
minimum_size_separators()
Returns a list containing all separator vertex sets of minimum size.
A vertex set is a separator if its removal disconnects the graph. This method
lists all the separators for which no smaller separator set exists in the given
graph.
Return Value
a list where each item lists the vertex indices of a given separator of
minimum size.
Reference: Arkady Kanevsky: Finding all minimum-size separating vertex
sets in a graph. Networks 23:533541, 1993.

195

Class GraphBase

Package igraph

modularity(membership, weights=None)
Calculates the modularity of the graph with respect to some vertex types.
The modularity of a graph w.r.t. some division measures how good the
division is, or how separated are the different vertex types from each other. It
is defined as Q=1/(2m) * sum(Aij-ki*kj/(2m)delta(ci,cj),i,j). m is the number
of edges, Aij is the element of the A adjacency matrix in row i and column j,
ki is the degree of node i, kj is the degree of node j, and Ci and cj are the
types of the two vertices (i and j ). delta(x,y) is one iff x=y, 0 otherwise.
If edge weights are given, the definition of modularity is modified as follows:
Aij becomes the weight of the corresponding edge, ki is the total weight of
edges incident on vertex i, kj is the total weight of edges incident on vertex j
and m is the total edge weight in the graph.
Parameters
membership: the membership vector, e.g. the vertex type index for
each vertex.
weights:

optional edge weights or None if all edges are weighed

equally.

Return Value
the modularity score. Score larger than 0.3 usually indicates strong
community structure.
Attention: method overridden in Graph to allow VertexClustering objects
as a parameter. This method is not strictly necessary, since the
VertexClustering class provides a variable called modularity.
Reference: MEJ Newman and M Girvan: Finding and evaluating community
structure in networks. Phys Rev E 69 026113, 2004.

196

Class GraphBase

Package igraph

motifs_randesu(size=3, cut_prob=None, callback =None)

Counts the number of motifs in the graph
Motifs are small subgraphs of a given structure in a graph. It is argued that
the motif profile (ie. the number of different motifs in the graph) is
characteristic for different types of networks and network function is related to
the motifs in the graph.
This function is able to find the different motifs of size three and four (ie. the
number of different subgraphs with three and four vertices) in the network.
In a big network the total number of motifs can be very large, so it takes a lot
of time to find all of them. In such cases, a sampling method can be used.
This function is capable of doing sampling via the cut_prob argument. This
argument gives the probability that a branch of the motif search tree will not
be explored.
Parameters
size:

the size of the motifs (3 or 4).

cut_prob: the cut probabilities for different levels of the search tree.
This must be a list of length size or None to find all
motifs.
callback: None or a callable that will be called for every motif
found in the graph. The callable must accept three
parameters: the graph itself, the list of vertices in the
motif and the isomorphy class of the motif (see
Graph.isoclass()). The search will stop when the
callback returns an object with a non-zero truth value or
raises an exception.
Return Value
the list of motifs if callback is None, or None otherwise
Reference: S. Wernicke and F. Rasche: FANMOD: a tool for fast network
motif detection, Bioinformatics 22(9), 11521153, 2006.
See Also: Graph.motifs_randesu_no()

197

Class GraphBase

Package igraph

motifs_randesu_estimate(size=3, cut_prob=None, sample)

Counts the total number of motifs in the graph
Motifs are small subgraphs of a given structure in a graph. This function
estimates the total number of motifs in a graph without assigning isomorphism
classes to them by extrapolating from a random sample of vertices.
Parameters
size:

the size of the motifs (3 or 4).

cut_prob: the cut probabilities for different levels of the search tree.
This must be a list of length size or None to find all
motifs.
sample:

the size of the sample or the vertex IDs of the vertices to

be used for sampling.

Reference: S. Wernicke and F. Rasche: FANMOD: a tool for fast network

motif detection, Bioinformatics 22(9), 11521153, 2006.
See Also: Graph.motifs_randesu()
motifs_randesu_no(size=3, cut_prob=None)
Counts the total number of motifs in the graph
Motifs are small subgraphs of a given structure in a graph. This function
counts the total number of motifs in a graph without assigning isomorphism
classes to them.
Parameters
size:

the size of the motifs (3 or 4).

cut_prob: the cut probabilities for different levels of the search tree.
This must be a list of length size or None to find all
motifs.
Reference: S. Wernicke and F. Rasche: FANMOD: a tool for fast network
motif detection, Bioinformatics 22(9), 11521153, 2006.
See Also: Graph.motifs_randesu()

198

Class GraphBase

Package igraph

neighborhood(vertices=None, order =1, mode=ALL)

For each vertex specified by vertices, returns the vertices reachable from that
vertex in at most order steps.
Parameters
vertices: a single vertex ID or a list of vertex IDs, or None
meaning all the vertices in the graph.
mode:

specifies how to take into account the direction of the

edges if a directed graph is analyzed. "out" means that
only the outgoing edges are followed, so all vertices
reachable from the source vertex in at most order steps
are counted. "in" means that only the incoming edges
are followed (in reverse direction of course), so all
vertices from which the source vertex is reachable in at
most order steps are counted. "all" treats directed
edges as undirected.

Return Value
a single list specifying the neighborhood if vertices was an integer
specifying a single vertex index, or a list of lists if vertices was a list
or None.
neighborhood_size(vertices=None, order =1, mode=ALL)
For each vertex specified by vertices, returns the number of vertices reachable
from that vertex in at most order steps.
Parameters
vertices: a single vertex ID or a list of vertex IDs, or None
meaning all the vertices in the graph.
mode:

specifies how to take into account the direction of the

Return Value
a single number specifying the neighborhood size if vertices was an
integer specifying a single vertex index, or a list of sizes if vertices
was a list or None.

199

Class GraphBase

Package igraph

neighbors(vertex, mode=ALL)
Returns adjacent vertices to a given vertex.
Parameters
vertex: a vertex ID
mode:

whether to return only predecessors (OUT), successors (IN)

or both (ALL). Ignored for undirected graphs.

path_length_hist(directed =True)
Calculates the path length histogram of the graph
Parameters
directed: whether to consider directed paths
Return Value
a tuple. The first item of the tuple is a list of path lengths, the ith
element of the list contains the number of paths with length i+1.
The second item contains the number of unconnected vertex pairs as
a float (since it might not fit into an integer)
Attention: this function is wrapped in a more convenient syntax in the
derived class Graph. It is advised to use that instead of this version.
permute_vertices(permutation)
Permutes the vertices of the graph according to the given permutation and
returns the new graph.
Vertex k of the original graph will become vertex permutation[k] in the new
graph. No validity checks are performed on the permutation vector.
Return Value
the new graph

200

Class GraphBase

Package igraph

personalized_pagerank(vertices=None, directed =True, damping=0.85,

reset=None, reset_vertices=None, weights=None, arpack_options=None,
implementation="prpack", niter =1000, eps=0.001)
Calculates the personalized PageRank values of a graph.
The personalized PageRank calculation is similar to the PageRank calculation,
but the random walk is reset to a non-uniform distribution over the vertices in
every step with probability 1-damping instead of a uniform distribution.
Parameters
vertices:

the indices of the vertices being queried. None

means all of the vertices.

directed:

whether to consider directed paths.

damping:

the damping factor. 1-damping is the PageRank

value for vertices with no incoming links.

reset:

the distribution over the vertices to be used when

resetting the random walk. Can be a sequence, an
iterable or a vertex attribute name as long as
they return a list of floats whose length is equal
to the number of vertices. If None, a uniform
distribution is assumed, which makes the method
equivalent to the original PageRank algorithm.

reset_vertices: an alternative way to specify the distribution over

the vertices to be used when resetting the random
walk. Simply supply a list of vertex IDs here, or a
VertexSeq or a Vertex. Resetting will take place
using a uniform distribution over the specified
vertices.
weights:

edge weights to be used. Can be a sequence or

iterable or even an edge attribute name.

arpack_options: an ARPACKOptions object used to fine-tune the

ARPACK eigenvector calculation. If omitted, the
module-level variable called arpack_options is
used. This argument is ignored if not the
ARPACK implementation is used, see the
implementation argument.
implementation: which implementation to use to solve the
PageRank eigenproblem. Possible values are:
"prpack": use the PRPACK library. This is a
new implementation in igraph 0.7
"arpack": use the ARPACK library. This
implementation was used from version 0.5,
until version 0.7.
201
"power": use
a simple power method. This is
the implementation that was used before
igraph version 0.5.
niter:

The number of iterations to use in the power

Class GraphBase

Package igraph

predecessors(vertex )
Returns the predecessors of a given vertex.
Equivalent to calling the Graph.neighbors method with type=IN.
radius(mode=OUT)
Calculates the radius of the graph.
The radius of a graph is defined as the minimum eccentricity of its vertices
(see eccentricity()).
Parameters
mode: what kind of paths to consider for the calculation in case of
directed graphs. OUT considers paths that follow edge
directions, IN considers paths that follow the opposite edge
directions, ALL ignores edge directions. The argument is
ignored for undirected graphs.
Return Value
the radius@see: Graph.eccentricity()
reciprocity(ignore_loops=True, mode="default")
Reciprocity defines the proportion of mutual connections in a directed graph.
It is most commonly defined as the probability that the opposite counterpart
of a directed edge is also included in the graph. This measure is calculated if
mode is "default".
Prior to igraph 0.6, another measure was implemented, defined as the
probability of mutual connection between a vertex pair if we know that there
is a (possibly non-mutual) connection between them. In other words,
(unordered) vertex pairs are classified into three groups: (1) disconnected, (2)
non-reciprocally connected and (3) reciprocally connected. The result is the
size of group (3), divided by the sum of sizes of groups (2) and (3). This
measure is calculated if mode is "ratio".
Parameters
ignore_loops: whether loop edges should be ignored.
mode:

the algorithm to use to calculate the reciprocity; see

above for more details.

Return Value
the reciprocity of the graph

202

Class GraphBase

Package igraph

rewire(n=1000, mode="simple")
Randomly rewires the graph while preserving the degree distribution.
Please note that the rewiring is done "in-place", so the original graph will be
modified. If you want to preserve the original graph, use the copy method
before.
Parameters
n:
the number of rewiring trials.
mode: the rewiring algorithm to use. It can either be "simple" or
"loops"; the former does not create or destroy loop edges
while the latter does.
rewire_edges(prob, loops=False, multiple=False)
Rewires the edges of a graph with constant probability.
Each endpoint of each edge of the graph will be rewired with a constant
probability, given in the first argument.
Please note that the rewiring is done "in-place", so the original graph will be
modified. If you want to preserve the original graph, use the copy method
before.
Parameters
prob:
loops:

rewiring probability
whether the algorithm is allowed to create loop edges

multiple: whether the algorithm is allowed to create multiple edges.

203

Class GraphBase

Package igraph

shortest_paths(source=None, target=None, weights=None, mode=OUT)

Calculates shortest path lengths for given vertices in a graph.
The algorithm used for the calculations is selected automatically: a simple
BFS is used for unweighted graphs, Dijkstras algorithm is used when all the
weights are positive. Otherwise, the Bellman-Ford algorithm is used if the
number of requested source vertices is larger than 100 and Johnsons algorithm
is used otherwise.
Parameters
source: a list containing the source vertex IDs which should be
included in the result. If None, all vertices will be
considered.
target: a list containing the target vertex IDs which should be
included in the result. If None, all vertices will be
considered.
weights: a list containing the edge weights. It can also be an
attribute name (edge weights are retrieved from the given
attribute) or None (all edges have equal weight).
mode:

the type of shortest paths to be used for the calculation in

directed graphs. OUT means only outgoing, IN means only
incoming paths. ALL means to consider the directed graph
as an undirected one.

Return Value
the shortest path lengths for given vertices in a matrix

204

Class GraphBase

Package igraph

similarity_dice(vertices=None, pairs=None, mode=IGRAPH_ALL,

loops=True)
Dice similarity coefficient of vertices.
The Dice similarity coefficient of two vertices is twice the number of their
common neighbors divided by the sum of their degrees. This coefficient is very
similar to the Jaccard coefficient, but usually gives higher similarities than its
counterpart.
Parameters
vertices: the vertices to be analysed. If None and pairs is also
None, all vertices will be considered.
pairs:

the vertex pairs to be analysed. If this is given, vertices

must be None, and the similarity values will be
calculated only for the given pairs. Vertex pairs must be
specified as tuples of vertex IDs.

mode:

which neighbors should be considered for directed graphs.

Can be ALL, IN or OUT, ignored for undirected graphs.

loops:

whether vertices should be considered adjacent to

themselves. Setting this to True assumes a loop edge for
all vertices even if none is present in the graph. Setting
this to False may result in strange results: nonadjacent
vertices may have larger similarities compared to the
case when an edge is added between them however,
this might be exactly the result you want to get.

Return Value
the pairwise similarity coefficients for the vertices specified, in the
form of a matrix if pairs is None or in the form of a list if pairs is
not None.

205

Class GraphBase

Package igraph

similarity_inverse_log_weighted(vertices=None, mode=IGRAPH_ALL)
Inverse log-weighted similarity coefficient of vertices.
Each vertex is assigned a weight which is 1 / log(degree). The log-weighted
similarity of two vertices is the sum of the weights of their common neighbors.
Parameters
vertices: the vertices to be analysed. If None, all vertices will be
considered.
mode:

which neighbors should be considered for directed

graphs. Can be ALL, IN or OUT, ignored for undirected
graphs. IN means that the weights are determined by the
out-degrees, OUT means that the weights are determined
by the in-degrees.

Return Value
the pairwise similarity coefficients for the vertices specified, in the
form of a matrix (list of lists).

206

Class GraphBase

Package igraph

similarity_jaccard(vertices=None, pairs=None, mode=IGRAPH_ALL,

loops=True)
Jaccard similarity coefficient of vertices.
The Jaccard similarity coefficient of two vertices is the number of their
common neighbors divided by the number of vertices that are adjacent to at
least one of them.
Parameters
vertices: the vertices to be analysed. If None and pairs is also
None, all vertices will be considered.
pairs:

the vertex pairs to be analysed. If this is given, vertices

must be None, and the similarity values will be
calculated only for the given pairs. Vertex pairs must be
specified as tuples of vertex IDs.

mode:

which neighbors should be considered for directed graphs.

Can be ALL, IN or OUT, ignored for undirected graphs.

loops:

whether vertices should be considered adjacent to

Return Value
the pairwise similarity coefficients for the vertices specified, in the
form of a matrix if pairs is None or in the form of a list if pairs is
not None.

207

Class GraphBase

Package igraph

simplify(multiple=True, loops=True, combine_edges=None)

Simplifies a graph by removing self-loops and/or multiple edges.
For example, suppose you have a graph with an edge attribute named weight.
graph.simplify(combine_edges=max) will take the maximum of the weights
of multiple edges and assign that weight to the collapsed edge.
graph.simplify(combine_edges=sum) will take the sum of the weights. You
can also write graph.simplify(combine_edges=dict(weight="sum")) or
graph.simplify(combine_edges=dict(weight=sum)), since sum is
recognised both as a Python built-in function and as a string constant.
Parameters
multiple:
loops:

whether to remove multiple edges.

whether to remove loops.

combine_edges: specifies how to combine the attributes of multiple

edges between the same pair of vertices into a
single attribute. If it is None, only one of the edges
will be kept and all the attributes will be lost. If it
is a function, the attributes of multiple edges will
be collected and passed on to that function which
will return the new attribute value that has to be
assigned to the single collapsed edge. It can also be
one of the following string constants:
"ignore": all the edge attributes will be
ignored.
"sum": the sum of the edge attribute values
will be used for the new edge.
"product": the product of the edge attribute
values will be used for the new edge.
"mean": the mean of the edge attribute values
will be used for the new edge.
"median": the median of the edge attribute
values will be used for the new edge.
"min": the minimum of the edge attribute
values will be used for the new edge.
"max": the maximum of the edge attribute
values will be used for the new edge.
"first": the attribute value of the first edge in
the collapsed set will be used for the new edge.
"last": the attribute value of the last edge in
the collapsed set will be used for the new edge.
"random": a randomly selected value will be
used for the new edge
208attribute values will be
"concat": the
concatenated for the new edge.
You can also use a dict mapping edge attribute
names to functions or the above string constants if

Class GraphBase

Package igraph

st_mincut(source, target, capacity=None)

Calculates the minimum cut between the source and target vertices in a graph.
Parameters
source:

the source vertex ID

target:

the target vertex ID

capacity: the capacity of the edges. It must be a list or a valid

attribute name or None. In the latter case, every edge
will have the same capacity.
Return Value
the value of the minimum cut, the IDs of vertices in the first and
second partition, and the IDs of edges in the cut, packed in a 4-tuple
Attention: this function has a more convenient interface in class Graph which
wraps the result in a list of Cut objects. It is advised to use that.
strength(vertices, mode=ALL, loops=True, weights=None)
Returns the strength (weighted degree) of some vertices from the graph
This method accepts a single vertex ID or a list of vertex IDs as a parameter,
and returns the strength (that is, the sum of the weights of all incident edges)
of the given vertices (in the form of a single integer or a list, depending on the
input parameter).
Parameters
vertices: a single vertex ID or a list of vertex IDs
mode:

the type of degree to be returned (OUT for out-degrees,

IN IN for in-degrees or ALL for the sum of them).

loops:

whether self-loops should be counted.

weights: edge weights to be used. Can be a sequence or iterable or

even an edge attribute name.

209

Class GraphBase

Package igraph

subcomponent(v, mode=ALL)
Determines the indices of vertices which are in the same component as a given
vertex.
Parameters
v:
the index of the vertex used as the source/destination
mode: if equals to IN, returns the vertex IDs from where the given
vertex can be reached. If equals to OUT, returns the vertex
IDs which are reachable from the given vertex. If equals to
ALL, returns all vertices within the same component as the
given vertex, ignoring edge directions. Note that this is not
equal to calculating the union of the results of IN and OUT.
Return Value
the indices of vertices which are in the same component as a given
vertex.
subgraph_edges(edges, delete_vertices=True)
Returns a subgraph spanned by the given edges.
Parameters
edges:

a list containing the edge IDs which should be

included in the result.

delete_vertices: if True, vertices not incident on any of the

specified edges will be deleted from the result. If
False, all vertices will be kept.
Return Value
the subgraph

210

Class GraphBase

Package igraph

subisomorphic_lad(other, domains=None, induced =False, time_limit=0,

return_mapping=False)
Checks whether a subgraph of the graph is isomorphic to another graph.
The optional domains argument may be used to restrict vertices that may
match each other. You can also specify whether you are interested in induced
subgraphs only or not.
Parameters
other:

the pattern graph we are looking for in the graph.

domains:

a list of lists, one sublist belonging to each vertex

in the template graph. Sublist i contains the
indices of the vertices in the original graph that
may match vertex i in the template graph. None
means that every vertex may match every other
vertex.

induced:

whether to consider induced subgraphs only.

time_limit:

an optimal time limit in seconds. Only the

integral part of this number is taken into account.
If the time limit is exceeded, the method will
throw an exception.

return_mapping: when True, the function will return a tuple, where

the first element is a boolean denoting whether a
subisomorphism has been found or not, and the
second element describes the mapping of the
vertices from the template graph to the original
graph. When False, only the boolean is returned.
Return Value
if no mapping is calculated, the result is True if the graph contains a
subgraph that is isomorphic to the given template, False otherwise.
If the mapping is calculated, the result is a tuple, the first element
being the above mentioned boolean, and the second element being
the mapping from the target to the original graph.

211

Class GraphBase

Package igraph

subisomorphic_vf2(other, color1 =None, color2 =None, edge_color1 =None,

edge_color2 =None, return_mapping_12 =False,
return_mapping_21 =False, callback =None, node_compat_fn=None,
edge_compat_fn=None)
Checks whether a subgraph of the graph is isomorphic to another graph.
Vertex and edge colors may be used to restrict the isomorphisms, as only
vertices and edges with the same color will be allowed to match each other.
Parameters
other:

the other graph with which we want to

compare the graph.

color1:

optional vector storing the coloring of the

vertices of the first graph. If None, all vertices
have the same color.

color2:

optional vector storing the coloring of the

vertices of the second graph. If None, all
vertices have the same color.

edge_color1:

optional vector storing the coloring of the

edges of the first graph. If None, all edges
have the same color.

edge_color2:

optional vector storing the coloring of the

edges of the second graph. If None, all edges
have the same color.

return_mapping_12: if True, calculates the mapping which maps

the vertices of the first graph to the second.
The mapping can contain -1 if a given node is
not mapped.
return_mapping_21: if True, calculates the mapping which maps
the vertices of the second graph to the first.
The mapping can contain -1 if a given node is
not mapped.
callback:

if not None, the subisomorphism search will

not stop at the first match; it will call this
callback function instead for every
subisomorphism found. The callback function
must accept four arguments: the first graph,
the second graph, a mapping from the nodes
of the first graph to the second, and a
mapping from the nodes of the second graph
to the first. The function must return True if
the search should continue or False otherwise.

node_compat_fn:

a function that receives the two graphs and

two node indices
212 (one from the first graph,
one from the second graph) and returns True
if the nodes given by the two indices are
compatible (i.e. they could be matched to
each other) or False otherwise. This can be

Class GraphBase

Package igraph

successors(vertex )
Returns the successors of a given vertex.
Equivalent to calling the Graph.neighbors method with type=OUT.
to_directed(mutual =True)
Converts an undirected graph to directed.
Parameters
mutual: True if mutual directed edges should be created for every
undirected edge. If False, a directed edge with arbitrary
direction is created.
to_undirected(mode="collapse", combine_edges=None)
Converts a directed graph to undirected.
Parameters
mode:

specifies what to do with multiple directed edges

going between the same vertex pair. True or
"collapse" means that only a single edge should
be created from multiple directed edges. False or
"each" means that every edge will be kept (with
the arrowheads removed). "mutual" creates one
undirected edge for each mutual directed edge pair.

combine_edges: specifies how to combine the attributes of multiple

edges between the same pair of vertices into a
single attribute. See Graph.simplify() for more
details.
topological_sorting(mode=OUT)
Calculates a possible topological sorting of the graph.
Returns a partial sorting and issues a warning if the graph is not a directed
acyclic graph.
Parameters
mode: if OUT, vertices are returned according to the forward
topological order all vertices come before their successors. If
IN, all vertices come before their ancestors.
Return Value
a possible topological ordering as a list

213

Class GraphBase

Package igraph

transitivity_avglocal_undirected(mode="nan")
Calculates the average of the vertex transitivities of the graph.
The transitivity measures the probability that two neighbors of a vertex are
connected. In case of the average local transitivity, this probability is
calculated for each vertex and then the average is taken. Vertices with less
than two neighbors require special treatment, they will either be left out from
the calculation or they will be considered as having zero transitivity,
depending on the mode parameter.
Note that this measure is different from the global transitivity measure (see
transitivity_undirected()) as it simply takes the average local transitivity
across the whole network.
Parameters
mode: defines how to treat vertices with degree less than two. If
TRANSITIVITT_ZERO or "zero", these vertices will have zero
transitivity. If TRANSITIVITY_NAN or "nan", these vertices
will be excluded from the average.
See Also: transitivity_undirected(),
transitivity_local_undirected()
Reference: D. J. Watts and S. Strogatz: Collective dynamics of small-world
networks. Nature 393(6884):440-442, 1998.

214

Class GraphBase

Package igraph

transitivity_local_undirected(vertices=None, mode="nan",
weights=None)
Calculates the local transitivity (clustering coefficient) of the given vertices in
the graph.
The transitivity measures the probability that two neighbors of a vertex are
connected. In case of the local transitivity, this probability is calculated
separately for each vertex.
Note that this measure is different from the global transitivity measure (see
transitivity_undirected()) as it calculates a transitivity value for each
vertex individually.
The traditional local transitivity measure applies for unweighted graphs only.
When the weights argument is given, this function calculates the weighted
local transitivity proposed by Barrat et al (see references).
Parameters
vertices: a list containing the vertex IDs which should be included
in the result. None means all of the vertices.
mode:

defines how to treat vertices with degree less than two. If

TRANSITIVITT_ZERO or "zero", these vertices will have
zero transitivity. If TRANSITIVITY_NAN or "nan", these
vertices will have NaN (not a number) as their transitivity.

weights: edge weights to be used. Can be a sequence or iterable or

even an edge attribute name.
Return Value
the transitivities for the given vertices in a list
See Also: transitivity_undirected(),
transitivity_avglocal_undirected()
Reference:
Watts DJ and Strogatz S: Collective dynamics of small-world
networks. Nature 393(6884):440-442, 1998.
Barrat A, Barthelemy M, Pastor-Satorras R and Vespignani A:
The architecture of complex weighted networks. PNAS 101, 3747
(2004). http://arxiv.org/abs/cond-mat/0311416 .

215

Class GraphBase

Package igraph

transitivity_undirected(mode="nan")
Calculates the global transitivity (clustering coefficient) of the graph.
The transitivity measures the probability that two neighbors of a vertex are
connected. More precisely, this is the ratio of the triangles and connected
triplets in the graph. The result is a single real number. Directed graphs are
considered as undirected ones.
Note that this measure is different from the local transitivity measure (see
transitivity_local_undirected()) as it calculates a single value for the
whole graph.
Parameters
mode: if TRANSITIVITY_ZERO or "zero", the result will be zero if
the graph does not have any triplets. If "nan" or
TRANSITIVITY_NAN, the result will be NaN (not a number).
Return Value
the transitivity
See Also: transitivity_local_undirected(),
transitivity_avglocal_undirected()
Reference: S. Wasserman and K. Faust: Social Network Analysis: Methods
and Applications. Cambridge: Cambridge University Press, 1994.
triad_census()
Triad census, as defined by Davis and Leinhardt
Calculating the triad census means classifying every triplets of vertices in a
directed graph. A triplet can be in one of 16 states, these are listed in the
documentation of the C interface of igraph.
Attention: this function has a more convenient interface in class Graph which
wraps the result in a TriadCensus object. It is advised to use that. The name
of the triplet classes are also documented there.

216

Class GraphBase

Package igraph

unfold_tree(sources=None, mode=OUT)
Unfolds the graph using a BFS to a tree by duplicating vertices as necessary.
Parameters
sources: the source vertices to start the unfolding from. It should
be a list of vertex indices, preferably one vertex from each
connected component. You can use
Graph.topological_sorting() to determine a suitable
set. A single vertex index is also accepted.
mode:

which edges to follow during the BFS. OUT follows

outgoing edges, IN follows incoming edges, ALL follows
both. Ignored for undirected graphs.

Return Value
the unfolded tree graph and a mapping from the new vertex indices
to the old ones.
union(graphs)
Creates the union of two (or more) graphs.
Parameters
graphs: the list of graphs to be united with the current one.
vcount()
Counts the number of vertices.
Return Value
the number of vertices in the graph.
(type=integer)
vertex_attributes()
Return Value
the attribute name list of the graphs vertices

217

Class GraphBase

Package igraph

vertex_connectivity(source=-1, target=-1, checks=True,

the source vertex involved in the calculation.

target:

the target vertex involved in the calculation.

checks:

if the whole graph connectivity is calculated and this is

neighbors: tells igraph what to do when the two vertices are

connected. "error" raises an exception, "infinity"
returns infinity, "ignore" ignores the edge.
Return Value
the vertex connectivity

218

Class GraphBase

Package igraph

write_dimacs(f, source, target, capacity=None)

Writes the graph in DIMACS format to the given file.
Parameters
f:

the name of the file to be written or a Python file handle

source:

the source vertex ID

target:

the target vertex ID

capacity: the capacities of the edges in a list. If it is not a list, the

corresponding edge attribute will be used to retrieve
capacities.
write_dot(f )
Writes the graph in DOT format to the given file.
DOT is the format used by the GraphViza software package.
Parameters
f: the name of the file to be written or a Python file handle
a http://www.graphviz.org

write_edgelist(f )
Writes the edge list of a graph to a file.
Directed edges are written in (from, to) order.
Parameters
f: the name of the file to be written or a Python file handle
write_gml(f, creator =None, ids=None)
Writes the graph in GML format to the given file.
Parameters
f:

the name of the file to be written or a Python file handle

creator: optional creator information to be written to the file. If

None, the current date and time is added.
ids:

optional numeric vertex IDs to use in the file. This must

be a list of integers or None. If None, the id attribute of
the vertices are used, or if they dont exist, numeric vertex
IDs will be generated automatically.

219

Class GraphBase

Package igraph

write_graphml(f )
Writes the graph to a GraphML file.
Parameters
f: the name of the file to be written or a Python file handle
write_leda(f, names="name", weights="weights")
Writes the graph to a file in LEDA native format.
The LEDA format supports at most one attribute per vertex and edge. You
can specify which vertex and edge attribute you want to use. Note that the
name of the attribute is not saved in the LEDA file.
Parameters
f:
names:

the name of the file to be written or a Python file handle

the name of the vertex attribute to be stored along with
the vertices. It is usually used to store the vertex names
(hence the name of the keyword argument), but you may
also use a numeric attribute. If you dont want to store
any vertex attributes, supply None here.

weights: the name of the edge attribute to be stored along with the
edges. It is usually used to store the edge weights (hence
the name of the keyword argument), but you may also use
a string attribute. If you dont want to store any edge
attributes, supply None here.
write_lgl(f, names="name", weights="weights", isolates=True)
Writes the edge list of a graph to a file in .lgl format.
Note that multiple edges and/or loops break the LGL software, but igraph
does not check for this condition. Unless you know that the graph does not
have multiple edges and/or loops, it is wise to call simplify() before saving.
Parameters
f:
names:

the name of the file to be written or a Python file handle

the name of the vertex attribute containing the name of
the vertices. If you dont want to store vertex names,
supply None here.

weights: the name of the edge attribute containing the weight of

the vertices. If you dont want to store weights, supply
None here.
isolates: whether to include isolated vertices in the output.

220

Class GraphBase

Package igraph

write_ncol(f, names="name", weights="weights")

Writes the edge list of a graph to a file in .ncol format.
Note that multiple edges and/or loops break the LGL software, but igraph
does not check for this condition. Unless you know that the graph does not
have multiple edges and/or loops, it is wise to call simplify() before saving.
Parameters
f:
names:

the name of the file to be written or a Python file handle

the name of the vertex attribute containing the name of
the vertices. If you dont want to store vertex names,
supply None here.

weights: the name of the edge attribute containing the weight of

the vertices. If you dont want to store weights, supply
None here.
write_pajek(f )
Writes the graph in Pajek format to the given file.
Parameters
f: the name of the file to be written or a Python file handle
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __reduce__(),
__reduce_ex__(), __repr__(), __setattr__(), __sizeof__(), __subclasshook__()
1.11.2

Properties

Name
Inherited from object
__class__

Description

221

Module igraph._igraph

Low-level Python interface for the igraph library. Should not be used directly.
Version: 0.7.0
2.1

Functions
convex_hull(vs, coords=False)
Calculates the convex hull of a given point set.
Parameters
vs:
the point set as a list of lists
coords: if True, the function returns the coordinates of the corners
of the convex hull polygon, otherwise returns the corner
indices.
Return Value
either the hulls corner coordinates or the point indices
corresponding to them, depending on the coords parameter.

222

Functions

Module igraph._igraph

is_degree_sequence(out_deg, in_deg=None)
Returns whether a list of degrees can be a degree sequence of some graph.
Note that it is not required for the graph to be simple; in other words, this
function may return True for degree sequences that can be realized using one
or more multiple or loop edges only.
In particular, this function checks whether
all the degrees are non-negative
for undirected graphs, the sum of degrees are even
for directed graphs, the two degree sequences are of the same length and
equal sums
Parameters
out_deg: the list of degrees. For directed graphs, this list must
contain the out-degrees of the vertices.
in_deg: the list of in-degrees for directed graphs. This parameter
must be None for undirected graphs.
Return Value
True if there exists some graph that can realize the given degree
sequence, False otherwise.@see: is_graphical_degree_sequence()
if you do not want to allow multiple or loop edges.
is_graphical_degree_sequence(out_deg, in_deg=None)
Returns whether a list of degrees can be a degree sequence of some simple
graph.
Note that it is required for the graph to be simple; in other words, this
function will return False for degree sequences that cannot be realized
without using one or more multiple or loop edges.
Parameters
out_deg: the list of degrees. For directed graphs, this list must
contain the out-degrees of the vertices.
in_deg: the list of in-degrees for directed graphs. This parameter
must be None for undirected graphs.
Return Value
True if there exists some simple graph that can realize the given
degree sequence, False otherwise.
See Also: is_degree_sequence() if you want to allow multiple or loop edges.

223

Variables

Module igraph._igraph

set_progress_handler(handler )
Sets the handler to be called when igraph is performing a long operation.
Parameters
handler: the progress handler function. It must accept two
arguments, the first is the message informing the user
about what igraph is doing right now, the second is the
actual progress information (a percentage).
set_random_number_generator(generator )
Sets the random number generator used by igraph.
Parameters
generator: the generator to be used. It must be a Python object
with at least three attributes: random, randint and
gauss. Each of them must be callable and their
signature and behaviour must be identical to
random.random, random.randint and random.gauss.
By default, igraph uses the random module for random
number generation, but you can supply your alternative
implementation here. If the given generator is None,
igraph reverts to the default Mersenne twister generator
implemented in the C layer, which might be slightly
faster than calling back to Python for random numbers,
but you cannot set its seed or save its state.
set_status_handler(handler )
Sets the handler to be called when igraph tries to display a status message.
This is used to communicate the progress of some calculations where no
reasonable progress percentage can be given (so it is not possible to use the
progress handler).
Parameters
handler: the status handler function. It must accept a single
argument, the message that informs the user about what
igraph is doing right now.
2.2

Variables
Name
ADJ_DIRECTED
ADJ_LOWER

Description
Value: 0
Value: 3
continued on next page

224

Variables

Name
ADJ_MAX
ADJ_MIN
ADJ_PLUS
ADJ_UNDIRECTED
ADJ_UPPER
ALL
BLISS_F
BLISS_FL
BLISS_FLM
BLISS_FM
BLISS_FS
BLISS_FSM
GET_ADJACENCY_BOTH
GET_ADJACENCY_LOWER
GET_ADJACENCY_UPPER
IN
OUT
REWIRING_SIMPLE
REWIRING_SIMPLE_LOOPS
STAR_IN
STAR_MUTUAL
STAR_OUT
STAR_UNDIRECTED
STRONG
TRANSITIVITY_NAN
TRANSITIVITY_ZERO
TREE_IN
TREE_OUT
TREE_UNDIRECTED
WEAK
__build_date__
__package__
arpack_options

Module igraph._igraph

Description
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:

1
4
5
1
2
3
0
1
4
3
2
5
2

Value: 1
Value: 0
Value:
Value:
Value:
Value:

2
1
0
1

Value: 1
Value: 3
Value: 0
Value: 2
Value: 2
Value: 0
Value: 1
Value: 1
Value: 0
Value: 2
Value: 1
Value: Apr 24 2014
Value: None
Value: <igraph.ARPACKOptions object at
0x7fc6738b8cd0>

225

Class InternalError

2.3

Module igraph._igraph

Class InternalError

object
exceptions.BaseException
exceptions.Exception
igraph._igraph.InternalError
2.3.1

Methods

Inherited from exceptions.Exception

__init__(), __new__()
Inherited from exceptions.BaseException
__delattr__(), __getattribute__(), __getitem__(), __getslice__(), __reduce__(), __repr__(), __setattr__(), __setstate__(), __str__(), __unicode__()
Inherited from object
__format__(), __hash__(), __reduce_ex__(), __sizeof__(), __subclasshook__()
2.3.2

Properties

Name
Inherited from exceptions.BaseException
args, message
Inherited from object
__class__

226

Description

Variables

Package igraph.app

User interfaces of igraph

3.1

Modules

shell: Command-line user interface of igraph

(Section 4, p. 222)
3.2

Variables
Name
__package__

Description
Value: None

227

Class TerminalController

Module igraph.app.shell

Command-line user interface of igraph

The command-line interface launches a Python shell with the igraph module automatically
imported into the main namespace. This is mostly a convenience module and it is used only
by the igraph command line script which executes a suitable Python shell and automatically
imports igraphs classes and functions in the top-level namespace.
Supported Python shells are:
IDLE shell (class IDLEShell)
IPython shell (class IPythonShell)
Classic Python shell (class ClassicPythonShell)
The shells are tried in the above mentioned preference order one by one, unless the global.shells
configuration key is set which overrides the default order. IDLE shell is only tried in Windows unless explicitly stated by global.shells, since Linux and Mac OS X users are likely
to invoke igraph from the command line.
Version: 0.7.0
4.1

Functions
main()
The main entry point for igraph when invoked from the command line shell

4.2

Variables
Name
__package__

4.3

Description
Value: igraph.app

Class TerminalController

A class that can be used to portably generate formatted output to a terminal.

TerminalController defines a set of instance variables whose values are initialized to the
control sequence necessary to perform a given action. These can be simply included in
normal output to the terminal:
>>>
>>>

term = TerminalController()
print This is +term.GREEN+green+term.NORMAL
228

Class TerminalController

Module igraph.app.shell

This is green

Alternatively, the render() method can used, which replaces ${action} with the string
required to perform action:
>>>

term = TerminalController()
term.render(This is ${GREEN}green${NORMAL})

>>> print

This is green

If the terminal doesnt support a given action, then the value of the corresponding instance
variable will be set to . As a result, the above code will still work on terminals that do not
support color, except that their output will not be colored. Also, this means that you can
test whether the terminal supports a given action by simply testing the truth value of the
corresponding instance variable:
>>>

term = TerminalController()
term.CLEAR_SCREEN:

>>> if
...

print This terminal supports clearning the screen.

...

Finally, if the width and height of the terminal are known, then they will be stored in the
COLS and LINES attributes.
Author: Edward Loper
4.3.1

Methods

__init__(self, term_stream=sys.stdout)
Create a TerminalController and initialize its attributes with appropriate
values for the current terminal. term_stream is the stream that will be used
for terminal output; if this stream is not a tty, then the terminal is assumed to
be a dumb terminal (i.e., have no capabilities).
render(self, template)
Replace each $-substitutions in the given template string with the
corresponding terminal control string (if its defined) or (if its not).

4.3.2

Class Variables

Name
BOL

Description
Move the cursor to the beginning of the line
Value:
continued on next page

229

Class TerminalController

Name
UP
DOWN
LEFT
RIGHT
CLEAR_SCREEN
CLEAR_EOL
CLEAR_BOL
CLEAR_EOS
BOLD
BLINK
DIM
REVERSE
NORMAL
HIDE_CURSOR
SHOW_CURSOR
COLS
LINES
WHITE
YELLOW
MAGENTA
RED
CYAN
GREEN
BLUE
BLACK

Module igraph.app.shell

Description
Move the cursor up one line
Value:
Move the cursor down one line
Value:
Move the cursor left one char
Value:
Move the cursor right one char
Value:
Clear the screen and move to home position
Value:
Clear to the end of the line.
Value:
Clear to the beginning of the line.
Value:
Clear to the end of the screen
Value:
Turn on bold mode
Value:
Turn on blink mode
Value:
Turn on half-bright mode
Value:
Turn on reverse-video mode
Value:
Turn off all modes
Value:
Make the cursor invisible
Value:
Make the cursor visible
Value:
Width of the terminal (None for unknown)
Value: None
Height of the terminal (None for unknown)
Value: None
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:
continued on next page

230

Class ProgressBar

Name
BG_CYAN
BG_GREEN
BG_BLUE
BG_BLACK
BG_WHITE
BG_YELLOW
BG_MAGENTA
BG_RED

4.4

Module igraph.app.shell

Description
Value:
Value:
Value:
Value:
Value:
Value:
Value:
Value:

Class ProgressBar

A 2-line progress bar, which looks like:

Header
20% [===========----------------------------------]
The progress bar is colored, if the terminal supports color output; and adjusts to the width
of the terminal.
4.4.1

Methods

__init__(self, term)
update(self, percent=None, message=None)
Updates the progress bar.
Parameters
percent: the percentage to be shown. If None, the previous value
will be used.
message: the message to be shown above the progress bar. If None,
the previous message will be used.
update_message(self, message)
Updates the message of the progress bar.
Parameters
message: the message to be shown above the progress bar
clear(self )
Clears the progress bar (i.e. removes it from the screen)
231

Class Shell

4.4.2

Module igraph.app.shell

Class Variables

Name
BAR
HEADER

4.4.3

Instance Variables

Name
cleared

4.5

Description
Value: %3d%%
${GREEN}[${BOLD}%s%s${NORMAL}${GREEN}]${NORMAL}
Value: ${BOLD}${CYAN}%s${NORMAL}\n

Description
true if we havent drawn the bar yet.

Class Shell

object
igraph.app.shell.Shell

Known Subclasses: igraph.app.shell.ClassicPythonShell, igraph.app.shell.IDLEShell, igraph.app.shell.IP

Superclass of the embeddable shells supported by igraph
4.5.1

Methods

__init__(self )
x.__init__(...) initializes x; see help(type(x)) for signature
Overrides: object.__init__ extit(inherited documentation)
__call__(self )
supports_progress_bar(self )
Checks whether the shell supports progress bars.
This is done by checking for the existence of an attribute called
_progress_handler.

232

Class IDLEShell

Module igraph.app.shell

supports_status_messages(self )
Checks whether the shell supports status messages.
This is done by checking for the existence of an attribute called
_status_handler.
get_progress_handler(self )
Returns the progress handler (if exists) or None (if not).
get_status_handler(self )
Returns the status handler (if exists) or None (if not).
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
4.5.2

Properties

Name
Inherited from object
__class__

4.6

Description

Class IDLEShell

object
igraph.app.shell.Shell
igraph.app.shell.IDLEShell
IDLE embedded shell interface.
This class allows igraph to be embedded in IDLE (the Tk Python IDE).
To Do: no progress bar support yet. Shell/Restart Shell command should re-import igraph
again.

233

Class ConsoleProgressBarMixin

4.6.1

Module igraph.app.shell

Methods

__init__(self )
Constructor.
Imports IDLEs embedded shell. The implementation of this method is ripped
from idlelib.PyShell.main() after removing the unnecessary parts.
Overrides: object.__init__
__call__(self )
Starts the shell
Overrides: igraph.app.shell.Shell.__call__
Inherited from igraph.app.shell.Shell(Section 4.5)

get_progress_handler(), get_status_handler(), supports_progress_bar(), supports_status_message

Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
4.6.2

Properties

Name
Inherited from object
__class__

4.7

Description

Class ConsoleProgressBarMixin

object
igraph.app.shell.ConsoleProgressBarMixin
Known Subclasses: igraph.app.shell.ClassicPythonShell, igraph.app.shell.IPythonShell
Mixin class for console shells that support a progress bar.

234

Class IPythonShell

4.7.1

Module igraph.app.shell

Methods

__init__(self )
x.__init__(...) initializes x; see help(type(x)) for signature
Overrides: object.__init__ extit(inherited documentation)
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
4.7.2

Properties

Name
Inherited from object
__class__

4.8

Description

Class IPythonShell

object
igraph.app.shell.Shell
object
igraph.app.shell.ConsoleProgressBarMixin
igraph.app.shell.IPythonShell
IPython embedded shell interface.
This class allows igraph to be embedded in IPythons interactive shell.

235

Class ClassicPythonShell

4.8.1

Module igraph.app.shell

Methods

__init__(self )
Constructor.
Imports IPythons embedded shell with separator lines removed.
Overrides: object.__init__
__call__(self )
Starts the embedded shell.
Overrides: igraph.app.shell.Shell.__call__
Inherited from igraph.app.shell.Shell(Section 4.5)

get_progress_handler(), get_status_handler(), supports_progress_bar(), supports_status_message

Properties

Name
Inherited from object
__class__

4.9

Description

Class ClassicPythonShell

object
igraph.app.shell.Shell
object
igraph.app.shell.ConsoleProgressBarMixin
igraph.app.shell.ClassicPythonShell
Classic Python shell interface.

236

Class ClassicPythonShell

Module igraph.app.shell

This class allows igraph to be embedded in Pythons shell.

4.9.1

Methods

__init__(self )
Constructor.
Imports Pythons classic shell
Overrides: object.__init__
__call__(self )
Starts the embedded shell.
Overrides: igraph.app.shell.Shell.__call__
Inherited from igraph.app.shell.Shell(Section 4.5)

get_progress_handler(), get_status_handler(), supports_progress_bar(), supports_status_message

Properties

Name
Inherited from object
__class__

Description

237

Module igraph.clustering

Classes related to graph clustering.

License: Copyright (C) 2006-2012 Tams Nepusz <ntamas@gmail.com> Pzmny Pter
stny 1/a, 1117 Budapest, Hungary
This program is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation; either version
2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program;
if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
MA 02110-1301 USA

238

Module igraph.clustering

239

Functions

5.1

Module igraph.clustering

Functions
compare_communities(comm1, comm2, method =vi,
remove_none=False)
Compares two community structures using various distance measures.
Parameters
comm1:

the first community structure as a membership list or

as a Clustering object.

comm2:

the second community structure as a membership list

or as a Clustering object.

method:

the measure to use. "vi" or "meila" means the

variation of information metric of Meila (2003),
"nmi" or "danon" means the normalized mutual
information as defined by Danon et al (2005),
"split-join" means the split-join distance of van
Dongen (2000), "rand" means the Rand index of
Rand (1971), "adjusted_rand" means the adjusted
Rand index of Hubert and Arabie (1985).

remove_none: whether to remove None entries from the membership

lists. This is handy if your Clustering object was
constructed using
VertexClustering.FromAttribute using an
attribute which was not defined for all the vertices. If
remove_none is False, a None entry in either comm1
or comm2 will result in an exception. If remove_none
is True, None values are filtered away and only the
remaining lists are compared.
Return Value
the calculated measure.
Reference:
Meila M: Comparing clusterings by the variation of information.
In: Scholkopf B, Warmuth MK (eds). Learning Theory and
Kernel Machines: 16th Annual Conference on Computational
Learning Theory and 7th Kernel Workship, COLT/Kernel 2003,
Washington, DC, USA. Lecture Notes in Computer Science, vol.
2777, Springer, 2003. ISBN: 978-3-540-40720-1.
Danon L, Diaz-Guilera A, Duch J, Arenas A: Comparing
community structure identification. J Stat Mech P09008, 2005.
van Dongen D: Performance criteria for graph clustering and
Markov cluster experiments. Technical Report INS-R0012,
National Research Institute for Mathematics and Computer
Science in the Netherlands, Amsterdam, May 2000.
Rand WM: Objective criteria 240
for the evaluation of clustering
methods. J Am Stat Assoc 66(336):846-850, 1971.
Hubert L and Arabie P: Comparing partitions. Journal of
Classification 2:193-218, 1985.

Functions

Module igraph.clustering

split_join_distance(comm1, comm2, remove_none=False)

Calculates the split-join distance between two community structures.
The split-join distance is a distance measure defined on the space of partitions
of a given set. It is the sum of the projection distance of one partition from
the other and vice versa, where the projection number of A from B is if
calculated as follows:
1. For each set in A, find the set in B with which it has the maximal
overlap, and take note of the size of the overlap.
2. Take the sum of the maximal overlap sizes for each set in A.
3. Subtract the sum from n, the number of elements in the partition.
Note that the projection distance is asymmetric, thats why it has to be
calculated in both directions and then added together. This function returns
the projection distance of comm1 from comm2 and the projection distance of
comm2 from comm1, and returns them in a pair. The actual split-join distance
is the sum of the two distances. The reason why it is presented this way is
that one of the elements being zero then implies that one of the partitions is a
subpartition of the other (and if it is close to zero, then one of the partitions is
close to being a subpartition of the other).
Parameters
comm1:
comm2:

the first community structure as a membership list or

as a Clustering object.
the second community structure as a membership list
or as a Clustering object.

remove_none: whether to remove None entries from the membership

Class Clustering

5.2

Module igraph.clustering

Variables
Name
__package__

5.3

Description
Value: igraph

Class Clustering

object
igraph.clustering.Clustering
Known Subclasses: igraph.clustering.VertexClustering
Class representing a clustering of an arbitrary ordered set.
This is now used as a base for VertexClustering, but it might be useful for other purposes
as well.
Members of an individual cluster can be accessed by the [] operator:
>>>
>>>

cl = Clustering([0,0,0,0,1,1,1,2,2,2,2])
cl[0]

[0, 1, 2, 3]

The membership vector can be accessed by the membership property:

>>>

cl.membership

[0, 0, 0, 0, 1, 1, 1, 2, 2, 2, 2]

The number of clusters can be retrieved by the len function:

>>>

len(cl)

You can iterate over the clustering object as if it were a regular list of clusters:
>>> for

cluster

cl:

print " ".join(str(idx) for

...

idx

cluster)

...
0 1 2 3
4 5 6
7 8 9 10

If you need all the clusters at once as lists, you can simply convert the clustering object to
a list:
>>>
>>>

cluster_list = list(cl)
print cluster_list
242

Class Clustering

Module igraph.clustering

[[0, 1, 2, 3], [4, 5, 6], [7, 8, 9, 10]]

5.3.1

Methods

init(self, membership, params=None)

Constructor.
Parameters
membership: the membership list that is, the cluster index in
which each element of the set belongs to.
params:

additional parameters to be stored in this objects

dictionary.

Overrides: object.__init__
__getitem__(self, idx )
Returns the members of the specified cluster.
Parameters
idx: the index of the cluster
Return Value
the members of the specified cluster as a list
Raises
IndexError if the index is out of bounds
__iter__(self )
Iterates over the clusters in this clustering.
This method will return a generator that generates the clusters one by one.
__len__(self )
Returns the number of clusters.
Return Value
the number of clusters
__str__(self )
str(x)
Overrides: object.__str__ extit(inherited documentation)

243

Class Clustering

Module igraph.clustering

as_cover(self )
Returns a Cover that contains the same clusters as this clustering.
compare_to(self, other, *args, **kwds)
Compares this clustering to another one using some similarity or distance
metric.
This is a convenience method that simply calls compare_communities with
the two clusterings as arguments. Any extra positional or keyword argument is
also forwarded to compare_communities.
size(self, idx )
Returns the size of a given cluster.
Parameters
idx: the cluster in which we are interested.
sizes(self, *args)
Returns the size of given clusters.
The indices are given as positional arguments. If there are no positional
arguments, the function will return the sizes of all clusters.
size_histogram(self, bin_width=1)
Returns the histogram of cluster sizes.
Parameters
bin_width: the bin width of the histogram
Return Value
a Histogram object

244

Class VertexClustering

Module igraph.clustering

summary(self, verbosity=0, width=None)

Returns the summary of the clustering.
The summary includes the number of items and clusters, and also the list of
members for each of the clusters if the verbosity is nonzero.
Parameters
verbosity: determines whether the cluster members should be
printed. Zero verbosity prints the number of items and
clusters only.
Return Value
the summary of the clustering as a string.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__subclasshook__()
5.3.2

Properties

Name
membership
n

Description
Returns the membership vector.
Returns the number of elements covered by this
clustering.

Inherited from object

__class__

5.4

Class VertexClustering

object
igraph.clustering.Clustering
igraph.clustering.VertexClustering
Known Subclasses: igraph.cut.Cut
The clustering of the vertex set of a graph.
This class extends Clustering by linking it to a specific Graph object and by optionally
storing the modularity score of the clustering. It also provides some handy methods like
getting the subgraph corresponding to a cluster and such.

245

Class VertexClustering

Module igraph.clustering

Note: since this class is linked to a Graph, destroying the graph by the del operator does not
free the memory occupied by the graph if there exists a VertexClustering that references
the Graph.
5.4.1

Methods

init(self, graph, membership=None, modularity=None, params=None,

modularity_params=None)
Creates a clustering object for a given graph.
Parameters
graph:

the graph that will be associated to the

clustering

membership:

the membership list. The length of the list

must be equal to the number of vertices in the
graph. If None, every vertex is assumed to
belong to the same cluster.

modularity:

the modularity score of the clustering. If

None, it will be calculated when needed.

params:

additional parameters to be stored in this

object.

modularity_params: arguments that should be passed to

246

Class VertexClustering

Module igraph.clustering

FromAttribute(cls, graph, attribute, intervals=None, params=None)

Creates a vertex clustering based on the value of a vertex attribute.
Vertices having the same attribute will correspond to the same cluster.
Parameters
graph:

the graph on which we are working

attribute: name of the attribute on which the clustering is based.

intervals: for numeric attributes, you can either pass a single
number or a list of numbers here. A single number
means that the vertices will be put in bins of that width
and vertices ending up in the same bin will be in the
same cluster. A list of numbers specify the bin positions
explicitly; e.g., [10, 20, 30] means that there will be
four categories: vertices with the attribute value less
than 10, between 10 and 20, between 20 and 30 and
over 30. Intervals are closed from the left and open
from the right.
params:

additional parameters to be stored in this object.

Return Value
a new VertexClustering object
as_cover(self )
Returns a VertexCover that contains the same clusters as this clustering.
Overrides: igraph.clustering.Clustering.as_cover

247

Class VertexClustering

Module igraph.clustering

cluster_graph(self, combine_vertices=None, combine_edges=None)

Returns a graph where each cluster is contracted into a single vertex.
In the resulting graph, vertex i represents cluster i in this clustering. Vertex i
and j will be connected if there was at least one connected vertex pair (a, b)
in the original graph such that vertex a was in cluster i and vertex b was in
cluster j.
Parameters
combine_vertices: specifies how to derive the attributes of the
vertices in the new graph from the attributes of
the old ones. See Graph.contract_vertices()
for more details.
combine_edges:

specifies how to derive the attributes of the

edges in the new graph from the attributes of
the old ones. See Graph.simplify() for more
details. If you specify False here, edges will
not be combined, and the number of edges
between the vertices representing the original
clusters will be equal to the number of edges
between the members of those clusters in the
original graph.

Return Value
the new graph.
crossing(self )
Returns a boolean vector where element i is True iff edge i lies between
clusters, False otherwise.
recalculate_modularity(self )
Recalculates the stored modularity value.
This method must be called before querying the modularity score of the
clustering through the class member modularity or q if the graph has been
modified (edges have been added or removed) since the creation of the
VertexClustering object.
Return Value
the new modularity score

248

Class VertexClustering

Module igraph.clustering

subgraph(self, idx )
Get the subgraph belonging to a given cluster.
Parameters
idx: the cluster index
Return Value
a copy of the subgraph
Precondition: the vertex set of the graph hasnt been modified since the
moment the clustering was constructed.
subgraphs(self )
Gets all the subgraphs belonging to each of the clusters.
Return Value
a list containing copies of the subgraphs
Precondition: the vertex set of the graph hasnt been modified since the
moment the clustering was constructed.
giant(self )
Returns the giant community of the clustered graph.
The giant component a community for which no larger community exists.
Return Value
a copy of the giant community.
Note: there can be multiple giant communities, this method will return the
copy of an arbitrary one if there are multiple giant communities.
Precondition: the vertex set of the graph hasnt been modified since the
moment the clustering was constructed.

249

Class VertexClustering

Module igraph.clustering

plot(self, context, bbox, palette, *args, **kwds)

Plots the clustering to the given Cairo context in the given bounding box.
This is done by calling Graph.__plot__() with the same arguments, but
coloring the graph vertices according to the current clustering (unless
overridden by the vertex_color argument explicitly).
This method understands all the positional and keyword arguments that are
understood by Graph.__plot__(), only the differences will be highlighted
here:
mark_groups: whether to highlight some of the vertex groups by colored
polygons. Besides the values accepted by Graph.__plot__ (i.e., a dict
mapping colors to vertex indices, a list containing lists of vertex indices,
or False), the following are also accepted:
True: all the groups will be highlighted, the colors matching the
corresponding color indices from the current palette (see the palette
keyword argument of Graph.__plot__.
A dict mapping cluster indices or tuples of vertex indices to color
names. The given clusters or vertex groups will be highlighted by the
given colors.
A list of cluster indices. This is equivalent to passing a dict mapping
numeric color indices from the current palette to cluster indices;
therefore, the cluster referred to by element i of the list will be
highlighted by color i from the palette.
The value of the plotting.mark_groups configuration key is also taken
into account here; if that configuration key is True and mark_groups is
not given explicitly, it will automatically be set to True.
In place of lists of vertex indices, you may also use VertexSeq instances.
In place of color names, you may also use color indices into the current
palette. None as a color name will mean that the corresponding group is
ignored.
palette: the palette used to resolve numeric color indices to RGBA
values. By default, this is an instance of ClusterColoringPalette.
See Also: Graph.__plot__() for more supported keyword arguments.
Inherited from igraph.clustering.Clustering(Section 5.3)
__getitem__(), __iter__(), __len__(), __str__(), compare_to(), size(),
size_histogram(), sizes(), summary()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
250

Class Dendrogram

Module igraph.clustering

reduce(), __reduce_ex(), repr(), setattr(), sizeof__(),

__subclasshook__()
5.4.2

Properties

Name
Description
modularity
Returns the modularity score
q
Returns the modularity score
graph
Returns the graph belonging to this object
Inherited from igraph.clustering.Clustering (Section 5.3)
membership, n
Inherited from object
__class__

5.5

Class Dendrogram

object
igraph.clustering.Dendrogram
Known Subclasses: igraph.clustering.VertexDendrogram
The hierarchical clustering (dendrogram) of some dataset.
A hierarchical clustering means that we know not only the way the elements are separated
into groups, but also the exact history of how individual elements were joined into larger
subgroups.
This class internally represents the hierarchy by a matrix with n rows and 2 columns or
more precisely, a list of lists of size 2. This is exactly the same as the original format used
by igraphs C core. The ith row of the matrix contains the indices of the two clusters being
joined in time step i. The joint group will be represented by the ID n+i, with i starting
from one. The ID of the joint group will be referenced in the upcoming steps instead of any
of its individual members. So, IDs less than or equal to n (where n is the number of rows
in the matrix) mean the original members of the dataset (with ID from 0 to n), while IDs
up from n+1 mean joint groups. As an example, take a look at the dendrogram and the
internal representation of a given clustering of five nodes:
0 -+
|
1 -+-+
|
2 ---+-+
|

<====>

[[0, 1], [3, 4], [2, 5], [6, 7]]

251

Class Dendrogram

Module igraph.clustering

3 -+
|
|
|
4 -+---+--5.5.1

Methods

__init__(self, merges)
Creates a hierarchical clustering.
Parameters
merges: the merge history either in matrix or tuple format
Overrides: object.__init__
__str__(self )
str(x)
Overrides: object.__str__ extit(inherited documentation)
format(self, format=newick)
Formats the dendrogram in a foreign format.
Currently only the Newick format is supported.
Example:
>>>
>>>

d = Dendrogram([(2, 3), (0, 1), (4, 5)])

d.format()

((2,3)4,(0,1)5)6;
>>>
>>>

d.names = list("ABCDEFG")
d.format()

((C,D)E,(A,B)F)G;

252

Class Dendrogram

Module igraph.clustering

summary(self, verbosity=0, max_leaf_count=40)

Returns the summary of the dendrogram.
The summary includes the number of leafs and branches, and also an ASCII
art representation of the dendrogram unless it is too large.
Parameters
verbosity:

determines whether the ASCII representation of

the dendrogram should be printed. Zero verbosity
prints only the number of leafs and branches.

max_leaf_count: the maximal number of leafs to print in the

ASCII representation. If the dendrogram has
more leafs than this limit, the ASCII
representation will not be printed even if the
verbosity is larger than or equal to 1.
Return Value
the summary of the dendrogram as a string.
__plot__(self, context, bbox, palette, *args, **kwds)
Draws the dendrogram on the given Cairo context
Supported keyword arguments are:
orientation: the orientation of the dendrogram. Must be one of the
following values: left-right, bottom-top, right-left or top-bottom.
Individual elements are always placed at the former edge and merges are
performed towards the latter edge. Possible aliases: horizontal =
left-right, vertical = bottom-top, lr = left-right, rl =
right-left, tb = top-bottom, bt = bottom-top. The default is
left-right.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__subclasshook__()
5.5.2

Properties

Name
merges
names

Description
Returns the performed merges in matrix format
Returns the names of the nodes in the
dendrogram
continued on next page

253

Class VertexDendrogram

Module igraph.clustering

Name
Inherited from object
__class__

5.6

Description

Class VertexDendrogram

object
igraph.clustering.Dendrogram
igraph.clustering.VertexDendrogram
The dendrogram resulting from the hierarchical clustering of the vertex set of a graph.
5.6.1

Methods

init(self, graph, merges, optimal_count=None, params=None,

modularity_params=None)
Creates a dendrogram object for a given graph.
Parameters
graph:

the graph that will be associated to the

clustering

merges:

the merges performed given in matrix form.

optimal_count:

the optimal number of clusters where the

dendrogram should be cut. This is a hint
usually provided by the clustering algorithm
that produces the dendrogram. None means
that such a hint is not available; the optimal
count will then be selected based on the
modularity in such a case.

params:

additional parameters to be stored in this

object.

modularity_params: arguments that should be passed to

Class VertexDendrogram

Module igraph.clustering

as_clustering(self, n=None)
Cuts the dendrogram at the given level and returns a corresponding
VertexClustering object.
Parameters
n: the desired number of clusters. Merges are replayed from the
beginning until the membership vector has exactly n distinct
elements or until there are no more recorded merges, whichever
happens first. If None, the optimal count hint given by the
clustering algorithm will be used If the optimal count was not
given either, it will be calculated by selecting the level where the
modularity is maximal.
Return Value
a new VertexClustering object.
__plot__(self, context, bbox, palette, *args, **kwds)
Draws the vertex dendrogram on the given Cairo context
See Dendrogram.__plot__ for the list of supported keyword arguments.
Overrides: igraph.clustering.Dendrogram.__plot__
Inherited from igraph.clustering.Dendrogram(Section 5.5)
__str__(), format(), summary()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__subclasshook__()
5.6.2

Properties

Name
optimal_count

Description
Returns the optimal number of clusters for this
dendrogram.
If an optimal count hint was given at
construction time, this property simply returns
the hint. If such a count was not given, this
method calculates the optimal number of
clusters by maximizing the modularity along all
the possible cuts in the dendrogram.
Inherited from igraph.clustering.Dendrogram (Section 5.5)
merges, names
continued on next page

255

Class Cover

Module igraph.clustering

Name
Inherited from object
__class__

5.7

Description

Class Cover

object
igraph.clustering.Cover
Known Subclasses: igraph.clustering.VertexCover
Class representing a cover of an arbitrary ordered set.
Covers are similar to clusterings, but each element of the set may belong to more than one
cluster in a cover, and elements not belonging to any cluster are also allowed.
Cover instances provide a similar API as Clustering instances; for instance, iterating over
a Cover will iterate over the clusters just like with a regular Clustering instance. However,
they are not derived from each other or from a common superclass, and there might be
functions that exist only in one of them or the other.
Clusters of an individual cover can be accessed by the [] operator:
>>>
>>>

cl = Cover([[0,1,2,3], [2,3,4], [0,1,6]])

cl[0]

[0, 1, 2, 3]

The membership vector can be accessed by the membership property. Note that contrary
to Clustering instances, the membership vector will contain lists that contain the cluster
indices each item belongs to:
>>>

cl.membership

[[0, 2], [0, 2], [0, 1], [0, 1], [1], [], [2]]

The number of clusters can be retrieved by the len function:

>>>

len(cl)

You can iterate over the cover as if it were a regular list of clusters:
>>> for
...

cluster

cl:

print " ".join(str(idx) for

idx

cluster)

...
0 1 2 3
2 3 4

256

Class Cover

Module igraph.clustering

0 1 6

If you need all the clusters at once as lists, you can simply convert the cover to a list:
>>>
>>>

cluster_list = list(cl)
print cluster_list

[[0, 1, 2, 3], [2, 3, 4], [0, 1, 6]]

Clustering objects can readily be converted to Cover objects using the constructor:
>>>
>>>
>>>

clustering = Clustering([0, 0, 0, 0, 1, 1, 1, 2, 2, 2])

cover = Cover(clustering)
list(clustering) == list(cover)

True

5.7.1

Methods

init(self, clusters, n=0)

Constructs a cover with the given clusters.
Parameters
clusters: the clusters in this cover, as a list or iterable. Each
cluster is specified by a list or tuple that contains the IDs
of the items in this cluster. IDs start from zero.
n:

the total number of elements in the set that is covered by

this cover. If it is less than the number of unique
elements found in all the clusters, we will simply use the
number of unique elements, so it is safe to leave this at
zero. You only have to specify this parameter if there are
some elements that are covered by none of the clusters.

Overrides: object.__init__
__getitem__(self, index )
Returns the cluster with the given index.
__iter__(self )
Iterates over the clusters in this cover.
__len__(self )
Returns the number of clusters in this cover.

257

Class Cover

Module igraph.clustering

__str__(self )
Returns a string representation of the cover.
Overrides: object.__str__
size(self, idx )
Returns the size of a given cluster.
Parameters
idx: the cluster in which we are interested.
sizes(self, *args)
Returns the size of given clusters.
The indices are given as positional arguments. If there are no positional
arguments, the function will return the sizes of all clusters.
size_histogram(self, bin_width=1)
Returns the histogram of cluster sizes.
Parameters
bin_width: the bin width of the histogram
Return Value
a Histogram object
summary(self, verbosity=0, width=None)
Returns the summary of the cover.
The summary includes the number of items and clusters, and also the list of
members for each of the clusters if the verbosity is nonzero.
Parameters
verbosity: determines whether the cluster members should be
printed. Zero verbosity prints the number of items and
clusters only.
Return Value
the summary of the cover as a string.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__subclasshook__()

258

Class VertexCover

5.7.2

Module igraph.clustering

Properties

Name
membership

Description
Returns the membership vector of this cover.
The membership vector of a cover covering n
elements is a list of length n, where element i
contains the cluster indices of the ith item.
Returns the number of elements in the set
covered by this cover.

n
Inherited from object
__class__

5.8

Class VertexCover

object
igraph.clustering.Cover
igraph.clustering.VertexCover
Known Subclasses: igraph.clustering.CohesiveBlocks
The cover of the vertex set of a graph.
This class extends Cover by linking it to a specific Graph object. It also provides some handy
methods like getting the subgraph corresponding to a cluster and such.
Note: since this class is linked to a Graph, destroying the graph by the del operator does
not free the memory occupied by the graph if there exists a VertexCover that references the
Graph.
5.8.1

Methods

init(self, graph, clusters=None)

Creates a cover object for a given graph.
Parameters
graph:

the graph that will be associated to the cover

clusters: the list of clusters. If None, it is assumed that there is

only a single cluster that covers the whole graph.
Overrides: object.__init__

259

Class VertexCover

Module igraph.clustering

crossing(self )
Returns a boolean vector where element i is True iff edge i lies between
clusters, False otherwise.
subgraph(self, idx )
Get the subgraph belonging to a given cluster.
Parameters
idx: the cluster index
Return Value
a copy of the subgraph
Precondition: the vertex set of the graph hasnt been modified since the
moment the cover was constructed.
subgraphs(self )
Gets all the subgraphs belonging to each of the clusters.
Return Value
a list containing copies of the subgraphs
Precondition: the vertex set of the graph hasnt been modified since the
moment the cover was constructed.

260

Class VertexCover

Module igraph.clustering

plot(self, context, bbox, palette, *args, **kwds)

Plots the cover to the given Cairo context in the given bounding box.
This is done by calling Graph.__plot__() with the same arguments, but
drawing nice colored blobs around the vertex groups.
This method understands all the positional and keyword arguments that are
understood by Graph.__plot__(), only the differences will be highlighted
here:
mark_groups: whether to highlight the vertex clusters by colored
polygons. Besides the values accepted by Graph.__plot__ (i.e., a dict
mapping colors to vertex indices, a list containing lists of vertex indices,
or False), the following are also accepted:
True: all the clusters will be highlighted, the colors matching the
corresponding color indices from the current palette (see the palette
keyword argument of Graph.__plot__.
A dict mapping cluster indices or tuples of vertex indices to color
names. The given clusters or vertex groups will be highlighted by the
given colors.
A list of cluster indices. This is equivalent to passing a dict mapping
numeric color indices from the current palette to cluster indices;
therefore, the cluster referred to by element i of the list will be
highlighted by color i from the palette.
The value of the plotting.mark_groups configuration key is also taken
into account here; if that configuration key is True and mark_groups is
not given explicitly, it will automatically be set to True.
In place of lists of vertex indices, you may also use VertexSeq instances.
In place of color names, you may also use color indices into the current
palette. None as a color name will mean that the corresponding group is
ignored.
palette: the palette used to resolve numeric color indices to RGBA
values. By default, this is an instance of ClusterColoringPalette.
See Also: Graph.__plot__() for more supported keyword arguments.
Inherited from igraph.clustering.Cover(Section 5.7)
__getitem__(), __iter__(), __len__(), __str__(), size(), size_histogram(),
sizes(), summary()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
261

Class CohesiveBlocks

Module igraph.clustering

__subclasshook__()
5.8.2

Properties

Name

Description
graph
Returns the graph belonging to this object
Inherited from igraph.clustering.Cover (Section 5.7)
membership, n
Inherited from object
__class__

5.9

Class CohesiveBlocks

object
igraph.clustering.Cover
igraph.clustering.VertexCover
igraph.clustering.CohesiveBlocks
The cohesive block structure of a graph.
Instances of this type are created by Graph.cohesive_blocks(). See the documentation of
Graph.cohesive_blocks() for an explanation of what cohesive blocks are.
This class provides a few more methods that make handling of cohesive block structures
easier.

262

Class CohesiveBlocks

5.9.1

Module igraph.clustering

Methods

init(self, graph, blocks=None, cohesion=None, parent=None)

Constructs a new cohesive block structure for the given graph.
If any of blocks, cohesion or parent is None, all the arguments will be ignored
and Graph.cohesive_blocks() will be called to calculate the cohesive blocks.
Otherwise, these three variables should describe the *result* of a cohesive
block structure calculation. Chances are that you never have to construct
CohesiveBlocks instances directly, just use Graph.cohesive_blocks().
Parameters
graph:
blocks:

the graph itself

a list containing the blocks; each block is described as a
list containing vertex IDs.

cohesion: the cohesion of each block. The length of this list must
be equal to the length of blocks.
parent:

the parent block of each block. Negative values or None

mean that there is no parent block for that block. There
should be only one parent block, which covers the entire
graph.

Overrides: object.__init__
See Also: Graph.cohesive_blocks()
cohesion(self, idx )
Returns the cohesion of the group with the given index.
cohesions(self )
Returns the list of cohesion values for each group.
hierarchy(self )
Returns a new graph that describes the hierarchical relationships between the
groups.
The new graph will be a directed tree; an edge will point from vertex i to
vertex j if group i is a superset of group j. In other words, the edges point
downwards.

263

Class CohesiveBlocks

Module igraph.clustering

max_cohesion(self, idx )
Finds the maximum cohesion score among all the groups that contain the
given vertex.
max_cohesions(self )
For each vertex in the graph, returns the maximum cohesion score among all
the groups that contain the vertex.
parent(self, idx )
Returns the parent group index of the group with the given index or None if
the given group is the root.
parents(self )
Returns the list of parent group indices for each group or None if the given
group is the root.
__plot__(self, context, bbox, palette, *args, **kwds)
Plots the cohesive block structure to the given Cairo context in the given
bounding box.
Since a CohesiveBlocks instance is also a VertexCover, keyword arguments
accepted by VertexCover.__plot__() are also accepted here. The only
difference is that the vertices are colored according to their maximal cohesions
by default, and groups are marked by colored blobs except the last group
which encapsulates the whole graph.
See the documentation of VertexCover.__plot__() for more details.
Overrides: igraph.clustering.VertexCover.__plot__
Inherited from igraph.clustering.VertexCover(Section 5.8)
crossing(), subgraph(), subgraphs()
Inherited from igraph.clustering.Cover(Section 5.7)
__getitem__(), __iter__(), __len__(), __str__(), size(), size_histogram(),
sizes(), summary()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__subclasshook__()
264

Class CohesiveBlocks

5.9.2

Module igraph.clustering

Properties

Name
Description
Inherited from igraph.clustering.VertexCover (Section 5.8)
graph
Inherited from igraph.clustering.Cover (Section 5.7)
membership, n
Inherited from object
__class__

265

Variables

Module igraph.compat

Compatibility methods and backported versions of newer Python features to enable igraph
to run on Python 2.5.
License: Copyright (C) 2006-2012 Tams Nepusz <ntamas@gmail.com> Pzmny Pter
stny 1/a, 1117 Budapest, Hungary
This program is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation; either version
2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program;
if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
MA 02110-1301 USA
6.1

Variables
Name
__package__

Description
Value: igraph

266

Module igraph.configuration

Configuration framework for igraph.

igraph has some parameters which usually affect the behaviour of many functions. This
module provides the framework for altering and querying igraph parameters as well as saving
them to and retrieving them from disk.

License: Copyright (C) 2006-2012 Tam\xc3\xa1s Nepusz <ntamas@gmail.com> P\xc3\xa1zm\xc3\xa1ny

P\xc3\xa9ter s\xc3\xa9t\xc3\xa1ny 1/a, 1117 Budapest, Hungary
This program is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation; either version
2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program;
if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
MA 02110-1301 USA
7.1

Functions
get_platform_image_viewer()
Returns the path of an image viewer on the given platform
get_user_config_file()
Returns the path where the user-level configuration file is stored
init()
Default mechanism to initiate igraph configuration
This method loads the user-specific configuration file from the users home
directory, or if it does not exist, creates a default configuration.
The method is safe to be called multiple times, it will not parse the
configuration file twice.
Return Value
the Configuration object loaded or created.

267

Class Configuration

7.2

Module igraph.configuration

Variables
Name
__package__

7.3

Description
Value: igraph

Class Configuration

object
igraph.configuration.Configuration
Class representing igraph configuration details.
(section) General ideas
The configuration of igraph is stored in the form of name-value pairs. This object provides
an interface to the configuration data using the syntax known from dict:
>>>
>>>
>>>

c=Configuration()
c["general.verbose"] = True
print c["general.verbose"]

True

Configuration keys are organized into sections, and the name to be used for a given key is
always in the form section.keyname, like general.verbose in the example above. In that
case, general is the name of the configuration section, and verbose is the name of the key.
If the name of the section is omitted, it defaults to general, so general.verbose can be
referred to as verbose:
>>>
>>>
>>>

c=Configuration()
c["verbose"] = True
print c["general.verbose"]

True

User-level configuration is stored in ~/.igraphrc per default on Linux and Mac OS X

systems, or in C:\Documents and Settings\username\.igraphrc on Windows systems.
However, this configuration is read only when igraph is launched through its shell interface
defined in igraph.app.shell. This behaviour might change before version 1.0.
(section) Known configuration keys
The known configuration keys are presented below, sorted by section. When referring to
them in program code, dont forget to add the section name, expect in the case of section
general.
(section) General settings
268

Class Configuration

Module igraph.configuration

These settings are all stored in section general.

shells: the list of preferred Python shells to be used with the command-line igraph
script. The shells in the list are tried one by one until any of them is found on the
system. igraph functions are then imported into the main namespace of the shell and
the shell is launched. Known shells and their respective class names to be used can be
found in igraph.app.shell. Example: IPythonShell, ClassicPythonShell. This
is the default, by the way.
verbose: whether igraph should talk more than really necessary. For instance, if set
to True, some functions display progress bars.
(section) Application settings
These settings specify the external applications that are possibly used by igraph. They are
all stored in section apps.
image_viewer: image viewer application. If set to an empty string, it will be determined automatically from the platform igraph runs on. On Mac OS X, it defaults to
the Preview application. On Linux, it chooses a viewer from several well-known Linux
viewers like gthumb, kuickview and so on (see the source code for the full list). On
Windows, it defaults to the systems built-in image viewer.
(section) Plotting settings
These settings specify the default values used by plotting functions. They are all stored in
section plotting.
layout: default graph layout algorithm to be used.
mark_groups: whether to mark the clusters by polygons when plotting a clustering
object.
palette: default palette to be used for converting integer numbers to colors. See
colors.Palette for more information. Valid palette names are stored in colors.palettes.
wrap_labels: whether to try to wrap the labels of the vertices automatically if they
dont fit within the vertex. Default: False.
(section) Remote repository settings
These settings specify how igraph should access remote graph repositories. Currently only
the Nexus repository is supported. All these settings are stored in section remote.
nexus.url: the root URL of the Nexus repository. Default: http://nexus.igraph.org.
(section) Shell settings
These settings specify options for external environments in which igraph is embedded (e.g.,
IPython and its Qt console). These settings are stored in section shell.
ipython.inlining.Plot: whether to show instances of the Plot class inline in IPythons
269

Class Configuration

Module igraph.configuration

console if the console supports it. Default: True

7.3.1

Methods

__init__(self, filename=None)
Creates a new configuration instance.
Parameters
filename: file or file pointer to be read. Can be omitted.
Overrides: object.__init__
__contains__(self, item)
Checks whether the given configuration item is set.
Parameters
item: the configuration key to check.
Return Value
True if the key has an associated value, False otherwise.
__getitem__(self, item)
Returns the given configuration item.
Parameters
item: the configuration key to retrieve.
Return Value
the configuration value
__setitem__(self, item, value)
Sets the given configuration item.
Parameters
item: the configuration key to set
value: the new value of the configuration key
__delitem__(self, item)
Deletes the given item from the configuration.
If the item has a default value, the default value is written back instead of the
current value. Without a default value, the item is really deleted.

270

Class Configuration

Module igraph.configuration

has_key(self, item)
Checks if the configuration has a given key.
Parameters
item: the key being sought
load(self, stream=None)
Loads the configuration from the given file.
Parameters
stream: name of a file or a file object. The configuration will be
loaded from here. Can be omitted, in this case, the
user-level configuration is loaded.
save(self, stream=None)
Saves the configuration.
Parameters
stream: name of a file or a file object. The configuration will be
saved there. Can be omitted, in this case, the user-level
configuration file will be overwritten.
instance(cls)
Returns the single instance of the configuration object.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
7.3.2

Properties

Name
filename

Description
Returns the filename associated to the object.
It is usually the name of the configuration file
that was used when creating the object.
Configuration.load always overwrites it with
the filename given to it. If None, the
configuration was either created from scratch or
it was updated from a stream without name
information.

Inherited from object

continued on next page

271

Class Configuration

Module igraph.configuration

Name
__class__

Description

272

Class Cut

Module igraph.cut

Classes representing cuts and flows on graphs.

License: Copyright (C) 2006-2012 Tam\xc3\xa1s Nepusz <ntamas@gmail.com> P\xc3\xa1zm\xc3\xa1ny

Variables
Name
__package__

8.2

Description
Value: igraph

Class Cut

object
igraph.clustering.Clustering
igraph.clustering.VertexClustering
igraph.cut.Cut
Known Subclasses: igraph.cut.Flow
A cut of a given graph.
This is a simple class used to represent cuts returned by Graph.mincut(), Graph.all_st_cuts()
and other functions that calculate cuts.
A cut is a special vertex clustering with only two clusters. Besides the usual VertexClustering
methods, it also has the following attributes:
value - the value (capacity) of the cut. It is equal to the number of edges if there are
273

Class Cut

Module igraph.cut

no capacities on the edges.

partition - vertex IDs in the parts created after removing edges in the cut
cut - edge IDs in the cut
es - an edge selector restricted to the edges in the cut.
You can use indexing on this object to obtain lists of vertex IDs for both sides of the partition.
This class is usually not instantiated directly, everything is taken care of by the functions
that return cuts.
Examples:
igraph import Graph
g = Graph.Ring(20)
mc = g.mincut()
print mc.value

>>> from
>>>
>>>
>>>
2.0

>>> print

min(map(len, mc))

1
>>>

mc.es["color"] =

"red"

274

Class Cut

8.2.1

Module igraph.cut

Methods

init(self, graph, value=None, cut=None, partition=None,

partition2 =None)
Initializes the cut.
This should not be called directly, everything is taken care of by the functions
that return cuts.
Parameters
graph:

the graph that will be associated to the

clustering

membership:

the membership list. The length of the list

must be equal to the number of vertices in the
graph. If None, every vertex is assumed to
belong to the same cluster.

modularity:

the modularity score of the clustering. If

None, it will be calculated when needed.

params:

additional parameters to be stored in this

object.

modularity_params: arguments that should be passed to

Graph.modularity when the modularity is
(re)calculated. If the original graph was
weighted, you should pass a dictionary
containing a weight key with the appropriate
value here.
Overrides: object.__init__
__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
__str__(self )
str(x)
Overrides: object.__str__ extit(inherited documentation)
Inherited from igraph.clustering.VertexClustering(Section 5.4)
FromAttribute(), __plot__(), as_cover(), cluster_graph(), crossing(), giant(),
recalculate_modularity(), subgraph(), subgraphs()
275

Class Flow

Module igraph.cut

Inherited from igraph.clustering.Clustering(Section 5.3)

__getitem__(), __iter__(), __len__(), compare_to(), size(), size_histogram(),
sizes(), summary()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __subclasshook__()
8.2.2

Properties

Name

Description
es
Returns an edge selector restricted to the cut
partition
Returns the vertex IDs partitioned according to
the cut
cut
Returns the edge IDs in the cut
value
Returns the sum of edge capacities in the cut
Inherited from igraph.clustering.VertexClustering (Section 5.4)
graph, modularity, q
Inherited from igraph.clustering.Clustering (Section 5.3)
membership, n
Inherited from object
__class__

8.3

Class Flow

object
igraph.clustering.Clustering
igraph.clustering.VertexClustering
igraph.cut.Cut
igraph.cut.Flow
A flow of a given graph.
This is a simple class used to represent flows returned by Graph.maxflow. It has the following
attributes:
graph - the graph on which this flow is defined
value - the value (capacity) of the flow
276

Class Flow

Module igraph.cut

flow - the flow values on each edge. For directed graphs, this is simply a list where
element i corresponds to the flow on edge i. For undirected graphs, the direction of
the flow is not constrained (since the edges are undirected), hence positive flow always
means a flow from the smaller vertex ID to the larger, while negative flow means a flow
from the larger vertex ID to the smaller.
cut - edge IDs in the minimal cut corresponding to the flow.
partition - vertex IDs in the parts created after removing edges in the cut
es - an edge selector restricted to the edges in the cut.
This class is usually not instantiated directly, everything is taken care of by Graph.maxflow.
Examples:
igraph import Graph
g = Graph.Ring(20)
mf = g.maxflow(0, 10)
print mf.value

>>> from
>>>
>>>
>>>
2.0
>>>

mf.es["color"] =

"red"

277

Class Flow

8.3.1

Module igraph.cut

Methods

init(self, graph, value, flow, cut, partition)

Initializes the flow.
This should not be called directly, everything is taken care of by
Graph.maxflow.
Parameters
graph:

the graph that will be associated to the

clustering

membership:

the membership list. The length of the list

must be equal to the number of vertices in the
graph. If None, every vertex is assumed to
belong to the same cluster.

modularity:

the modularity score of the clustering. If

None, it will be calculated when needed.

params:

additional parameters to be stored in this

object.

modularity_params: arguments that should be passed to

Class Flow

Module igraph.cut

getitem(), iter(), len(), compare_to(), size(), size_histogram(),

sizes(), summary()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __subclasshook__()
8.3.2

Properties

Name

Description
flow
Returns the flow values for each edge.
For directed graphs, this is simply a list where
element i corresponds to the flow on edge i. For
undirected graphs, the direction of the flow is
not constrained (since the edges are
undirected), hence positive flow always means a
flow from the smaller vertex ID to the larger,
while negative flow means a flow from the
larger vertex ID to the smaller.
Inherited from igraph.cut.Cut (Section 8.2)
cut, es, partition, value
Inherited from igraph.clustering.VertexClustering (Section 5.4)
graph, modularity, q
Inherited from igraph.clustering.Clustering (Section 5.3)
membership, n
Inherited from object
__class__

279

Class Matrix

Module igraph.datatypes

Additional auxiliary data types

License: Copyright (C) 2006-2012 Tam\xc3\xa1s Nepusz <ntamas@gmail.com> P\xc3\xa1zm\xc3\xa1ny

Variables
Name
__package__

9.2

Description
Value: igraph

Class Matrix

object
igraph.datatypes.Matrix
Simple matrix data type.
Of course there are much more advanced matrix data types for Python (for instance, the
ndarray data type of Numeric Python) and this implementation does not want to compete
with them. The only role of this data type is to provide a convenient interface for the
matrices returned by the Graph object (for instance, allow indexing with tuples in the case
of adjacency matrices and so on).

280

Class Matrix

9.2.1

Module igraph.datatypes

Methods

__init__(self, data=None)
Initializes a matrix.
Parameters
data: the elements of the matrix as a list of lists, or None to create
a 0x0 matrix.
Overrides: object.__init__
Fill(cls, value, *args)
Creates a matrix filled with the given value
Parameters
value: the value to be used
shape: the shape of the matrix. Can be a single integer, two
integers or a tuple. If a single integer is given here, the
matrix is assumed to be square-shaped.
Zero(cls, *args)
Creates a matrix filled with zeros.
Parameters
shape: the shape of the matrix. Can be a single integer, two
integers or a tuple. If a single integer is given here, the
matrix is assumed to be square-shaped.
Identity(cls, *args)
Creates an identity matrix.
Parameters
shape: the shape of the matrix. Can be a single integer, two
integers or a tuple. If a single integer is given here, the
matrix is assumed to be square-shaped.

281

Class Matrix

Module igraph.datatypes

__add__(self, other )
Adds the given value to the matrix.
Parameters
other: either a scalar or a matrix. Scalars will be added to each
element of the matrix. Matrices will be added together
elementwise.
Return Value
the result matrix
__eq__(self, other )
Checks whether a given matrix is equal to another one
__getitem__(self, i)
Returns a single item, a row or a column of the matrix
Parameters
i: if a single integer, returns the ith row as a list. If a slice, returns
the corresponding rows as another Matrix object. If a 2-tuple,
the first element of the tuple is used to select a row and the
second is used to select a column.
__hash__(self )
Returns a hash value for a matrix.
Overrides: object.__hash__
__iadd__(self, other )
In-place addition of a matrix or scalar.
__isub__(self, other )
In-place subtraction of a matrix or scalar.
__ne__(self, other )
Checks whether a given matrix is not equal to another one

282

Class Matrix

Module igraph.datatypes

__setitem__(self, i, value)
Sets a single item, a row or a column of the matrix
Parameters
i:
if a single integer, sets the ith row as a list. If a slice, sets
the corresponding rows from another Matrix object. If a
2-tuple, the first element of the tuple is used to select a row
and the second is used to select a column.
value: the new value
__sub__(self, other )
Subtracts the given value from the matrix.
Parameters
other: either a scalar or a matrix. Scalars will be subtracted from
each element of the matrix. Matrices will be subtracted
together elementwise.
Return Value
the result matrix
__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
__str__(self )
str(x)
Overrides: object.__str__ extit(inherited documentation)
__iter__(self )
Support for iteration.
This is actually implemented as a generator, so there is no need for a separate
iterator class. The generator returns copies of the rows in the matrix as lists
to avoid messing around with the internals. Feel free to do anything with the
copies, the changes wont be reflected in the original matrix.

283

Class Matrix

Module igraph.datatypes

plot(self, context, bbox, palette, **kwds)

Plots the matrix to the given Cairo context in the given box
Besides the usual self-explanatory plotting parameters (context, bbox,
palette), it accepts the following keyword arguments:
style: the style of the plot. boolean is useful for plotting matrices with
boolean (True/False or 0/1) values: False will be shown with a white
box and True with a black box. palette uses the given palette to
represent numbers by colors, the minimum will be assigned to palette
color index 0 and the maximum will be assigned to the length of the
palette. None draws transparent cell backgrounds only. The default style
is boolean (but it may change in the future). None values in the matrix
are treated specially in both cases: nothing is drawn in the cell
corresponding to None.
square: whether the cells of the matrix should be square or not. Default
is True.
grid_width: line width of the grid shown on the matrix. If zero or
negative, the grid is turned off. The grid is also turned off if the size of a
cell is less than three times the given line width. Default is 1. Fractional
widths are also allowed.
border_width: line width of the border drawn around the matrix. If zero
or negative, the border is turned off. Default is 1.
row_names: the names of the rows
col_names: the names of the columns.
values: values to be displayed in the cells. If None or False, no values
are displayed. If True, the values come from the matrix being plotted. If
it is another matrix, the values of that matrix are shown in the cells. In
this case, the shape of the value matrix must match the shape of the
matrix being plotted.
value_format: a format string or a callable that specifies how the values
should be plotted. If it is a callable, it must be a function that expects a
single value and returns a string. Example: "%#.2f" for floating-point
numbers with always exactly two digits after the decimal point. See the
Python documentation of the % operator for details on the format string.
If the format string is not given, it defaults to the str function.
If only the row names or the column names are given and the matrix is
square-shaped, the same names are used for both column and row names.

284

Class DyadCensus

Module igraph.datatypes

min(self, dim=None)
Returns the minimum of the matrix along the given dimension
Parameters
dim: the dimension. 0 means determining the column minimums, 1
means determining the row minimums. If None, the global
minimum is returned.
max(self, dim=None)
Returns the maximum of the matrix along the given dimension
Parameters
dim: the dimension. 0 means determining the column maximums, 1
means determining the row maximums. If None, the global
maximum is returned.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __new__(), __reduce__(),
__reduce_ex__(), __setattr__(), __sizeof__(), __subclasshook__()
9.2.2

Properties

Name
data
shape
Inherited from object
__class__

9.3

Description
Returns the data stored in the matrix as a list
of lists
Returns the shape of the matrix as a tuple

Class DyadCensus

object
tuple
igraph.datatypes.DyadCensus
Dyad census of a graph.
This is a pretty simple class - basically it is a tuple, but it allows the user to refer to its
individual items by the names mutual (or mut), asymmetric (or asy or asym or asymm) and
null.

285

Class DyadCensus

Module igraph.datatypes

Examples:
igraph import Graph
g=Graph.Erdos_Renyi(100, 0.2, directed=True)
dc=g.dyad_census()
print dc.mutual
#doctest:+SKIP

>>> from
>>>
>>>
>>>
179

>>> print

dc["asym"]

#doctest:+SKIP

1609
>>> print

tuple(dc), list(dc)

#doctest:+SKIP

(179, 1609, 3162) [179, 1609, 3162]

>>> print

sorted(dc.as_dict().items())

#doctest:+ELLIPSIS

[(asymmetric, ...), (mutual, ...), (null, ...)]

9.3.1

Methods

__getitem__(self, idx )
x[y]
Overrides: tuple.__getitem__ extit(inherited documentation)
__getattr__(self, attr )
__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
__str__(self )
str(x)
Overrides: object.__str__ extit(inherited documentation)
as_dict(self )
Converts the dyad census to a dict using the known dyad names.
Inherited from tuple
__add__(), __contains__(), __eq__(), __ge__(), __getattribute__(), __getnewargs__(), __getslice__(), __gt__(), __hash__(), __iter__(), __le__(),
__len__(), __lt__(), __mul__(), __ne__(), __new__(), __rmul__(),
__sizeof__(), count(), index()
286

Class TriadCensus

Module igraph.datatypes

Inherited from object

__delattr__(), __format__(), __init__(), __reduce__(), __reduce_ex__(),
__setattr__(), __subclasshook__()
9.3.2

Properties

Name
Inherited from object
__class__

9.4

Description

Class TriadCensus

object
tuple
igraph.datatypes.TriadCensus
Triad census of a graph.
This is a pretty simple class - basically it is a tuple, but it allows the user to refer to its
individual items by the following triad names:

003 the empty graph

012 a graph with a single directed edge (A > B, C)
102 a graph with a single mutual edge (A <-> B, C)
021D the binary out-tree (A < B > C)
021U the binary in-tree (A > B < C)
021C the directed line (A > B > C)
111D A <-> B < C
111U A <-> B > C
030T A > B < C, A > C
030C A < B < C, A > C
201 A <-> B <-> C
120D A < B > C, A <-> C
120U A > B < C, A <-> C
120C A > B > C, A <-> C
210C A > B <-> C, A <-> C
300 the complete graph (A <-> B <-> C, A <-> C)
287

Class TriadCensus

Module igraph.datatypes

Attribute and item accessors are provided. Due to the syntax of Python, attribute names
are not allowed to start with a number, therefore the triad names must be prepended with a
lowercase t when accessing them as attributes. This is not necessary with the item accessor
syntax.
Examples:
igraph import Graph
g=Graph.Erdos_Renyi(100, 0.2, directed=True)
tc=g.triad_census()
print tc.t003
#doctest:+SKIP

>>> from
>>>
>>>
>>>

39864
>>> print

tc["030C"]

#doctest:+SKIP

1206

9.4.1

Methods

__getitem__(self, idx )
x[y]
Overrides: tuple.__getitem__ extit(inherited documentation)
__getattr__(self, attr )
__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
__str__(self )
str(x)
Overrides: object.__str__ extit(inherited documentation)
Inherited from tuple
__add__(), __contains__(), __eq__(), __ge__(), __getattribute__(), __getnewargs__(), __getslice__(), __gt__(), __hash__(), __iter__(), __le__(),
__len__(), __lt__(), __mul__(), __ne__(), __new__(), __rmul__(),
__sizeof__(), count(), index()
Inherited from object
__delattr__(), __format__(), __init__(), __reduce__(), __reduce_ex__(),
288

Class UniqueIdGenerator

Module igraph.datatypes

__setattr__(), __subclasshook__()
9.4.2

Properties

Name
Inherited from object
__class__

9.5

Description

Class UniqueIdGenerator

object
igraph.datatypes.UniqueIdGenerator
A dictionary-like class that can be used to assign unique IDs to names (say, vertex names).
Usage:
>>>
>>>

gen = UniqueIdGenerator()
gen["A"]

0
>>>

gen["B"]

1
>>>

gen["C"]

2
>>>

gen["A"]

# Retrieving already existing ID

gen.add("D")

# Synonym of gen["D"]

0
>>>
3
>>>

len(gen)

# Number of already used IDs

4
>>> "C" in

gen

True
>>> "E" in

gen

False

289

Class UniqueIdGenerator

9.5.1

Module igraph.datatypes

Methods

init(self, id_generator =None, initial =None)

Creates a new unique ID generator. id_generator specifies how do we assign
new IDs to elements that do not have an ID yet. If it is None, elements will
be assigned integer identifiers starting from 0. If it is an integer, elements will
be assigned identifiers starting from the given integer. If it is an iterator or
generator, its next method will be called every time a new ID is needed.
Overrides: object.__init__
__contains__(self, item)
Checks whether item already has an ID or not.
__getitem__(self, item)
Retrieves the ID corresponding to item. Generates a new ID for item if it is
the first time we request an ID for it.
__setitem__(self, item, value)
Overrides the ID for item.
__len__(self )
"Returns the number of items
reverse_dict(self )
Returns the reverse mapping, i.e., the one that maps from generated IDs to
their corresponding objects
values(self )
Returns the values stored so far. If the generator generates items according to
the standard sorting order, the values returned will be exactly in the order
they were added. This holds for integer IDs for instance (but for many other
ID generators as well).
add(self, item)
Retrieves the ID corresponding to item. Generates a new ID for item if it is
the first time we request an ID for it.
Inherited from object

290

Class UniqueIdGenerator

Module igraph.datatypes

delattr(), format(), getattribute(), hash(), new(),

__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
9.5.2

Properties

Name
Inherited from object
__class__

Description

291

Package igraph.drawing

Drawing and plotting routines for IGraph.

Plotting is dependent on the pycairo library which provides Python bindings to the popular
Cairo library1 . This means that if you dont have pycairo2 installed, you wont be able to
use the plotting capabilities. However, you can still use Graph.write_svg to save the graph
to an SVG file and view it from Mozilla Firefox3 (free) or edit it in Inkscape4 (free), Skencil5
(formerly known as Sketch, also free) or Adobe Illustrator (not free, therefore Im not linking
to it :)).
License: GPL
10.1

Modules

baseclasses: Abstract base classes for the drawing routines.

(Section 11, p. 306)
colors: Color handling functions.
(Section 12, p. 310)
coord: Coordinate systems and related plotting routines
(Section 13, p. 323)
edge: Drawers for various edge styles in graph plots.
(Section 14, p. 326)
graph: Drawing routines to draw graphs.
(Section 15, p. 334)
metamagic: Auxiliary classes for the default graph drawer in igraph.
(Section 16, p. 341)
shapes: Shape drawing classes for igraph
(Section 17, p. 345)
text: Drawers for labels on plots.
(Section 18, p. 348)
utils: Utility classes for drawing routines.
(Section 19, p. 353)
vertex: Drawing routines to draw the vertices of graphs.
(Section 20, p. 364)
1 http://www.cairographics.org
2 http://www.cairographics.org/pycairo
3 http://www.mozilla.org/firefox
4 http://www.inkscape.org
5 http://www.skencil.org

292

Modules

Package igraph.drawing

293

Functions

10.2

Package igraph.drawing

Functions
plot(obj, target=None, bbox =(0, 0, 600, 600), *args, **kwds)
Plots the given object to the given target.
Positional and keyword arguments not explicitly mentioned here will be passed
down to the __plot__ method of the object being plotted. Since you are most
likely interested in the keyword arguments available for graph plots, see
Graph.__plot__ as well.
Parameters
obj:

the object to be plotted

target: the target where the object should be plotted. It can be

one of the following types:
None an appropriate surface will be created and the
object will be plotted there.
cairo.Surface the given Cairo surface will be used.
This can refer to a PNG image, an arbitrary window,
an SVG file, anything that Cairo can handle.
string a file with the given name will be created
and an appropriate Cairo surface will be attached to
it. The supported image formats are: PNG, PDF,
SVG and PostScript.
bbox:

the bounding box of the plot. It must be a tuple with

either two or four integers, or a BoundingBox object. If
this is a tuple with two integers, it is interpreted as the
width and height of the plot (in pixels for PNG images
and on-screen plots, or in points for PDF, SVG and
PostScript plots, where 72 pt = 1 inch = 2.54 cm). If this
is a tuple with four integers, the first two denotes the X
and Y coordinates of a corner and the latter two denoting
the X and Y coordinates of the opposite corner.

opacity: the opacity of the object being plotted. It can be used to

overlap several plots of the same graph if you use the
same layout for them for instance, you might plot a
graph with opacity 0.5 and then plot its spanning tree
over it with opacity 0.1. To achieve this, youll need to
modify the Plot object returned with Plot.add.
palette: the palette primarily used on the plot if the added objects
do not specify a private palette. Must be either an
igraph.drawing.colors.Palette object or a string
referring to a valid key of
igraph.drawing.colors.palettes (see module
igraph.drawing.colors) or None. In the latter case, the
294
default palette given by the configuration key
plotting.palette is used.
margin: the top, right, bottom, left margins as a 4-tuple. If it has
less than 4 elements or is a single float, the elements will

Class DefaultGraphDrawer

10.3

Package igraph.drawing

Class DefaultGraphDrawer

object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.graph.AbstractGraphDrawer
object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.baseclasses.AbstractCairoDrawer
igraph.drawing.graph.AbstractCairoGraphDrawer

igraph.drawing.graph.DefaultGraphDrawer
Class implementing the default visualisation of a graph.
The default visualisation of a graph draws the nodes on a 2D plane according to a given
Layout, then draws a straight or curved edge between nodes connected by edges. This is
the visualisation used when one invokes the plot() function on a Graph object.
See Graph.__plot__() for the keyword arguments understood by this drawer.

295

Class DefaultGraphDrawer

10.3.1

Package igraph.drawing

Methods

init(self, context, bbox, vertex_drawer_factory=<class

igraph.drawing.vertex.DefaultVertexDrawer>,
edge_drawer_factory=<class igraph.drawing.edge.ArrowEdgeDrawer>,
label_drawer_factory=<class igraph.drawing.text.TextDrawer>)
Constructs the graph drawer and associates it to the given Cairo context and
the given BoundingBox.
Parameters
context:
bbox:

the context on which we will draw

the bounding box within which we will
draw. Can be anything accepted by the
constructor of BoundingBox (i.e., a
2-tuple, a 4-tuple or a BoundingBox
object).

vertex_drawer_factory: a factory method that returns an

AbstractCairoVertexDrawer instance
bound to a given Cairo context. The
factory method must take three
parameters: the Cairo context, the
bounding box of the drawing area and
the palette to be used for drawing colored
vertices. The default vertex drawer is
DefaultVertexDrawer.
edge_drawer_factory:

a factory method that returns an

AbstractEdgeDrawer instance bound to
a given Cairo context. The factory
method must take two parameters: the
Cairo context and the palette to be used
for drawing colored edges. You can use
any of the actual AbstractEdgeDrawer
implementations here to control the style
of edges drawn by igraph. The default
edge drawer is ArrowEdgeDrawer.

label_drawer_factory: a factory method that returns a

TextDrawer instance bound to a given
Cairo context. The method must take
one parameter: the Cairo context. The
default label drawer is TextDrawer.
Overrides: object.__init__

296

Class BoundingBox

Package igraph.drawing

draw(self, graph, palette, *args, **kwds)

Abstract method, must be implemented in derived classes.
Overrides: igraph.drawing.baseclasses.AbstractDrawer.draw extit(inherited
documentation)
Inherited from igraph.drawing.graph.AbstractGraphDrawer
ensure_layout()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
10.3.2

Properties

Name
Description
Inherited from igraph.drawing.baseclasses.AbstractCairoDrawer (Section 11.3)
bbox
Inherited from object
__class__

10.4

Class BoundingBox

object
igraph.drawing.utils.Rectangle
igraph.drawing.utils.BoundingBox
Class representing a bounding box (a rectangular area) that encloses some objects.

297

Class BoundingBox

10.4.1

Package igraph.drawing

Methods

__ior__(self, other )
Replaces this bounding box with the union of itself and another.
Example:
>>> box1 = BoundingBox(10, 20, 50, 60)
>>> box2 = BoundingBox(70, 40, 100, 90)
>>> box1 |= box2
>>> print(box1)
BoundingBox(10.0, 20.0, 100.0, 90.0)
Overrides: igraph.drawing.utils.Rectangle.__ior__
__or__(self, other )
Takes the union of this bounding box with another.
The result is a bounding box which encloses both bounding boxes.
Example:
>>> box1 = BoundingBox(10, 20, 50, 60)
>>> box2 = BoundingBox(70, 40, 100, 90)
>>> box1 | box2
BoundingBox(10.0, 20.0, 100.0, 90.0)
Overrides: igraph.drawing.utils.Rectangle.__or__
Inherited from igraph.drawing.utils.Rectangle(Section 19.1)
__and__(), __bool__(), __eq__(), __hash__(), __init__(), __ne__(),
__nonzero__(), __repr__(), contract(), expand(), intersection(), isdisjoint(),
isempty(), translate(), union()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __new__(), __reduce__(),
__reduce_ex__(), __setattr__(), __sizeof__(), __str__(), __subclasshook__()
10.4.2

Properties

Name
Description
Inherited from igraph.drawing.utils.Rectangle (Section 19.1)
bottom, coords, height, left, midx, midy, right, shape, top, width
Inherited from object
continued on next page

298

Class Point

Package igraph.drawing

Name
__class__

10.5

Description

Class Point

object
tuple
igraph.drawing.utils.Point
Class representing a point on the 2D plane.
10.5.1

Methods

__new__(cls, x, y)
Creates a new point with the given coordinates
Return Value
a new object with type S, a subtype of T
Overrides: object.__new__
__repr__(self )
Returns a nicely formatted representation of the point
Overrides: object.__repr__
__getnewargs__(self )
Return self as a plain tuple. Used by copy and pickle.
Overrides: tuple.__getnewargs__
__add__(self, other )
Adds the coordinates of a point to another one
Overrides: tuple.__add__
__sub__(self, other )
Subtracts the coordinates of a point to another one

299

Class Point

Package igraph.drawing

__mul__(self, scalar )
Multiplies the coordinates by a scalar
Overrides: tuple.__mul__
__rmul__(self, scalar )
Multiplies the coordinates by a scalar
Overrides: tuple.__rmul__
__div__(self, scalar )
Divides the coordinates by a scalar
as_polar(self )
Returns the polar coordinate representation of the point.
Return Value
the radius and the angle in a tuple.
distance(self, other )
Returns the distance of the point from another one.
Example:
>>>
>>>
>>>

p1 = Point(5, 7)
p2 = Point(8, 3)
p1.distance(p2)

5.0

interpolate(self, other, ratio=0.5)

300

Class Rectangle

Package igraph.drawing

normalized(self )
Normalizes the coordinates of the point s.t. its length will be 1 after
normalization. Returns the normalized point.
sq_length(self )
Returns the squared length of the vector pointing from the origin to this point.
towards(self, other, distance=0)
Returns the point that is at a given distance from this point towards another
one.
FromPolar(cls, radius, angle)
Constructs a point from polar coordinates.
radius is the distance of the point from the origin; angle is the angle
between the X axis and the vector pointing to the point from the origin.
Inherited from tuple
__contains__(), __eq__(), __ge__(), __getattribute__(), __getitem__(),
__getslice__(), __gt__(), __hash__(), __iter__(), __le__(), __len__(),
__lt__(), __ne__(), __sizeof__(), count(), index()
Inherited from object
__delattr__(), __format__(), __init__(), __reduce__(), __reduce_ex__(),
__setattr__(), __str__(), __subclasshook__()
10.5.2

Properties

Name
x
y
Inherited from object
__class__

10.6

Description
Alias for field number 0
Alias for field number 1

Class Rectangle

object
igraph.drawing.utils.Rectangle
301

Class Rectangle

Package igraph.drawing

Known Subclasses: igraph.drawing.utils.BoundingBox

Class representing a rectangle.
10.6.1

Methods

__init__(self, *args)
Creates a rectangle.
The corners of the rectangle can be specified by either a tuple (four items, two
for each corner, respectively), four separate numbers (X and Y coordinates for
each corner) or two separate numbers (width and height, the upper left corner
is assumed to be at (0,0))
Overrides: object.__init__
contract(self, margins)
Contracts the rectangle by the given margins.
Return Value
a new Rectangle object.
expand(self, margins)
Expands the rectangle by the given margins.
Return Value
a new Rectangle object.
isdisjoint(self, other )
Returns True if the two rectangles have no intersection.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1.isdisjoint(r2)
False
>>> r2.isdisjoint(r1)
False
>>> r1.isdisjoint(r3)
True
>>> r3.isdisjoint(r1)
True
302

Class Rectangle

Package igraph.drawing

isempty(self )
Returns True if the rectangle is empty (i.e. it has zero width and height).
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(70, 70, 90, 90)
>>> r1.isempty()
False
>>> r2.isempty()
False
>>> r1.intersection(r2).isempty()
True
intersection(self, other )
Returns the intersection of this rectangle with another.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1.intersection(r2)
Rectangle(20.0, 20.0, 30.0, 30.0)
>>> r2 & r1
Rectangle(20.0, 20.0, 30.0, 30.0)
>>> r2.intersection(r1) == r1.intersection(r2)
True
>>> r1.intersection(r3)
Rectangle(0.0, 0.0, 0.0, 0.0)

303

Class Rectangle

Package igraph.drawing

__and__(self, other )
Returns the intersection of this rectangle with another.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1.intersection(r2)
Rectangle(20.0, 20.0, 30.0, 30.0)
>>> r2 & r1
Rectangle(20.0, 20.0, 30.0, 30.0)
>>> r2.intersection(r1) == r1.intersection(r2)
True
>>> r1.intersection(r3)
Rectangle(0.0, 0.0, 0.0, 0.0)
translate(self, dx, dy)
Translates the rectangle in-place.
Example:
>>>
>>>
>>>

r = Rectangle(10, 20, 50, 70)

r.translate(30, -10)
r

Rectangle(40.0, 10.0, 80.0, 60.0)

Parameters
dx: the X coordinate of the translation vector
dy: the Y coordinate of the translation vector

304

Class Rectangle

Package igraph.drawing

union(self, other )
Returns the union of this rectangle with another.
The resulting rectangle is the smallest rectangle that contains both rectangles.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1.union(r2)
Rectangle(10.0, 10.0, 50.0, 50.0)
>>> r2 | r1
Rectangle(10.0, 10.0, 50.0, 50.0)
>>> r2.union(r1) == r1.union(r2)
True
>>> r1.union(r3)
Rectangle(10.0, 10.0, 90.0, 90.0)
__or__(self, other )
Returns the union of this rectangle with another.
The resulting rectangle is the smallest rectangle that contains both rectangles.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1.union(r2)
Rectangle(10.0, 10.0, 50.0, 50.0)
>>> r2 | r1
Rectangle(10.0, 10.0, 50.0, 50.0)
>>> r2.union(r1) == r1.union(r2)
True
>>> r1.union(r3)
Rectangle(10.0, 10.0, 90.0, 90.0)

305

Class Rectangle

Package igraph.drawing

__ior__(self, other )
Expands this rectangle to include itself and another completely while still
being as small as possible.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1 |= r2
>>> r1
Rectangle(10.0, 10.0, 50.0, 50.0)
>>> r1 |= r3
>>> r1
Rectangle(10.0, 10.0, 90.0, 90.0)
__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
__eq__(self, other )
__ne__(self, other )
__bool__(self )
__nonzero__(self )
__hash__(self )
hash(x)
Overrides: object.__hash__ extit(inherited documentation)
Inherited from object
__delattr__(), __format__(), __getattribute__(), __new__(), __reduce__(),
__reduce_ex__(), __setattr__(), __sizeof__(), __str__(), __subclasshook__()
10.6.2

Properties

306

Class Plot

Package igraph.drawing

Name
coords

width
height
left
right
top
bottom
midx
midy
shape
Inherited from object
__class__

10.7

Description
The coordinates of the corners.
The coordinates are returned as a 4-tuple in the
following order: left edge, top edge, right edge,
bottom edge.
The width of the rectangle
The height of the rectangle
The X coordinate of the left side of the box
The X coordinate of the right side of the box
The Y coordinate of the top edge of the box
The Y coordinate of the bottom edge of the box
The X coordinate of the center of the box
The Y coordinate of the center of the box
The shape of the rectangle (width, height)

Class Plot

object
igraph.drawing.Plot
Class representing an arbitrary plot
Every plot has an associated surface object where the plotting is done. The surface is an
instance of cairo.Surface, a member of the pycairo library. The surface itself provides a
unified API to various plotting targets like SVG files, X11 windows, PostScript files, PNG
files and so on. igraph usually does not know on which surface it is plotting right now, since
pycairo takes care of the actual drawing. Everything thats supported by pycairo should
be supported by this class as well.
Current Cairo surfaces that Im aware of are:

cairo.GlitzSurface OpenGL accelerated surface for the X11 Window System.

cairo.ImageSurface memory buffer surface. Can be written to a PNG image file.
cairo.PdfSurface PDF document surface.
cairo.PsSurface PostScript document surface.
cairo.Win32Surface Microsoft Windows screen rendering.
cairo.XlibSurface X11 Window System screen rendering.

If you create a Plot object with a string given as the target surface, the string will be treated
as a filename, and its extension will decide which surface class will be used. Please note that
307

Class Plot

Package igraph.drawing

not all surfaces might be available, depending on your pycairo installation.

A Plot has an assigned default palette (see igraph.drawing.colors.Palette) which is
used for plotting objects.
A Plot object also has a list of objects to be plotted with their respective bounding boxes,
palettes and opacities. Palettes assigned to an object override the default palette of the plot.
Objects can be added by the Plot.add method and removed by the Plot.remove method.

308

Class Plot

10.7.1

Package igraph.drawing

Methods

init(self, target=None, bbox =None, palette=None, background =None)

Creates a new plot.
Parameters
target:

the target surface to write to. It can be one of the

following types:
None an appropriate surface will be created and
the object will be plotted there.
cairo.Surface the given Cairo surface will be
used.
string a file with the given name will be created
and an appropriate Cairo surface will be attached
to it.

bbox:

the bounding box of the surface. It is interpreted

differently with different surfaces: PDF and PS
surfaces will treat it as points (1 point = 1/72 inch).
Image surfaces will treat it as pixels. SVG surfaces
will treat it as an abstract unit, but it will mostly be
interpreted as pixels when viewing the SVG file in
Firefox.

palette:

the palette primarily used on the plot if the added

objects do not specify a private palette. Must be
either an igraph.drawing.colors.Palette object or
a string referring to a valid key of
igraph.drawing.colors.palettes (see module
igraph.drawing.colors) or None. In the latter case,
the default palette given by the configuration key
plotting.palette is used.

background: the background color. If None, the background will be

transparent. You can use any color specification here
that is understood by
igraph.drawing.colors.color_name_to_rgba.
Overrides: object.__init__

309

Class Plot

Package igraph.drawing

add(self, obj, bbox =None, palette=None, opacity=1.0, *args, **kwds)

Adds an object to the plot.
Arguments not specified here are stored and passed to the objects plotting
function when necessary. Since you are most likely interested in the arguments
acceptable by graphs, see Graph.__plot__ for more details.
Parameters
obj:
bbox:

the object to be added

the bounding box of the object. If None, the object will
fill the entire area of the plot.

palette: the color palette used for drawing the object. If the object
tries to get a color assigned to a positive integer, it will
use this palette. If None, defaults to the global palette of
the plot.
opacity: the opacity of the object being plotted, in the range
0.0-1.0
See Also: Graph.__plot__
remove(self, obj, bbox =None, idx =1)
Removes an object from the plot.
If the object has been added multiple times and no bounding box was
specified, it removes the instance which occurs idx th in the list of identical
instances of the object.
Parameters
obj: the object to be removed
bbox: optional bounding box specification for the object. If given,
only objects with exactly this bounding box will be
considered.
idx: if multiple objects match the specification given by obj and
bbox, only the idx th occurrence will be removed.
Return Value
True if the object has been removed successfully, False if the object
was not on the plot at all or idx was larger than the count of
occurrences
mark_dirty(self )
Marks the plot as dirty (should be redrawn)

310

Class Plot

Package igraph.drawing

redraw(self, context=None)
Redraws the plot
save(self, fname=None)
Saves the plot.
Parameters
fname: the filename to save to. It is ignored if the surface of the plot
is not an ImageSurface.
show(self )
Saves the plot to a temporary file and shows it.
_repr_svg_(self )
Returns an SVG representation of this plot as a string.
This method is used by IPython to display this plot inline.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
10.7.2

Properties

Name
background
bounding_box
height
surface
width

Description
Returns the background color of the plot. None
means a transparent background.
Returns the bounding box of the Cairo surface
as a BoundingBox object
Returns the height of the Cairo surface on
which the plot is drawn
Returns the Cairo surface on which the plot is
drawn
Returns the width of the Cairo surface on
which the plot is drawn

Inherited from object

__class__

311

Class AbstractDrawer

Module igraph.drawing.baseclasses

Abstract base classes for the drawing routines.

11.1

Variables
Name
__package__

11.2

Description
Value: igraph.drawing

Class AbstractDrawer

object
igraph.drawing.baseclasses.AbstractDrawer

Known Subclasses: igraph.drawing.graph.AbstractGraphDrawer, igraph.drawing.baseclasses.AbstractCa

igraph.drawing.vertex.AbstractVertexDrawer, igraph.drawing.baseclasses.AbstractXMLRPCDrawer
Abstract class that serves as a base class for anything that draws an igraph object.
11.2.1

Methods

draw(self, *args, **kwds)

Abstract method, must be implemented in derived classes.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __init__(),
__new__(), __reduce__(), __reduce_ex__(), __repr__(), __setattr__(),
__sizeof__(), __str__(), __subclasshook__()
11.2.2

Properties

Name
Inherited from object
__class__

Description

312

Class AbstractCairoDrawer

11.3

Module igraph.drawing.baseclasses

Class AbstractCairoDrawer

object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.baseclasses.AbstractCairoDrawer

Known Subclasses: igraph.drawing.graph.AbstractCairoGraphDrawer, igraph.drawing.vertex.AbstractC

igraph.drawing.text.TextDrawer, igraph.drawing.coord.CoordinateSystem, igraph.drawing.shapes.PolygonD
Abstract class that serves as a base class for anything that draws on a Cairo context within
a given bounding box.
A subclass of AbstractCairoDrawer is guaranteed to have an attribute named context that
represents the Cairo context to draw on, and an attribute named bbox for the BoundingBox
of the drawing area.
11.3.1

Methods

init(self, context, bbox )

Constructs the drawer and associates it to the given Cairo context and the
given BoundingBox.
Parameters
context: the context on which we will draw
bbox:

the bounding box within which we will draw. Can be

anything accepted by the constructor of BoundingBox
(i.e., a 2-tuple, a 4-tuple or a BoundingBox object).

Overrides: object.__init__
draw(self, *args, **kwds)
Abstract method, must be implemented in derived classes.
Overrides: igraph.drawing.baseclasses.AbstractDrawer.draw
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
11.3.2

Properties

313

Class AbstractXMLRPCDrawer

Name
bbox

Module igraph.drawing.baseclasses

Description
The bounding box of the drawing area where
this drawer will draw.

Inherited from object

__class__

11.4

Class AbstractXMLRPCDrawer

object
igraph.drawing.baseclasses.AbstractDrawer

igraph.drawing.baseclasses.AbstractXMLRPCDrawe

Known Subclasses: igraph.drawing.graph.CytoscapeGraphDrawer, igraph.drawing.graph.UbiGraphDraw

Abstract drawer that uses a remote service via XML-RPC to draw something on a remote
display.
11.4.1

Methods

init(self, url, service=None)

Constructs an abstract drawer using the XML-RPC service at the given URL.
Parameters
url:

the URL where the XML-RPC calls for the service should
be addressed to.

service: the name of the service at the XML-RPC address. If

None, requests will be directed to the server proxy object
constructed by xmlrpclib.ServerProxy; if not None, the
given attribute will be looked up in the server proxy
object.
Overrides: object.__init__
Inherited from igraph.drawing.baseclasses.AbstractDrawer(Section 11.2)
draw()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
314

Class AbstractXMLRPCDrawer

11.4.2

Module igraph.drawing.baseclasses

Properties

Name
Inherited from object
__class__

Description

315

Module igraph.drawing.colors

Color handling functions.

Functions
color_name_to_rgb(color, palette=None)
Converts a color given in one of the supported color formats to R-G-B values.
This is done by calling color_name_to_rgba and then throwing away the
alpha value.
See Also: color_name_to_rgba for more details about what formats are
understood by this function.

316

Functions

Module igraph.drawing.colors

color_name_to_rgba(color, palette=None)
Converts a color given in one of the supported color formats to R-G-B-A
values.
Examples:
>>>

color_name_to_rgba("red")

(1.0, 0.0, 0.0, 1.0)

>>>

color_name_to_rgba("#ff8000") == (1.0, 128/255.0, 0.0, 1.0)

True
>>>

color_name_to_rgba("#ff800080") == (1.0, 128/255.0, 0.0, 128/255.0)

True
>>>

color_name_to_rgba("#08f") == (0.0, 136/255.0, 1.0, 1.0)

True
>>>

color_name_to_rgba("rgb(100%,

50%, 0%)")

(1.0, 0.5, 0.0, 1.0)

>>>

color_name_to_rgba("rgba(100%,

50%, 0%, 25%)")

(1.0, 0.5, 0.0, 0.25)

>>>

color_name_to_rgba("hsla(120,

100%, 50%, 0.5)")

(0.0, 1.0, 0.0, 0.5)

>>>

color_name_to_rgba("hsl(60,

100%, 50%)")

(1.0, 1.0, 0.0, 1.0)

>>>

color_name_to_rgba("hsv(60,

100%, 100%)")

(1.0, 1.0, 0.0, 1.0)

Parameters
color:

the color to be converted in one of the following formats:

CSS3 color specification: #rrggbb, #rgb,
#rrggbbaa, #rgba, rgb(red, green, blue),
rgba(red, green, blue, alpha), hsl(hue,
saturation, lightness), hsla(hue, saturation,
lightness, alpha), hsv(hue, saturation, value)
and hsva(hue, saturation, value, alpha) where
the components are given as hexadecimal numbers in
the first four cases and as decimals or percentages
(0%-100%) in the remaining cases. Red, green and
blue components are between 0 and 255; hue is
between 0 and 360; saturation, lightness and value is
between 0 and 100; alpha is between 0 and 1.
Valid HTML color names, i.e. those that are
present in the HTML 4.0 specification
Valid X11 color names, see
http://en.wikipedia.org/wiki/X11_color_names
Red-green-blue components given separately in
either a comma-, slash- or whitespace-separated string
or a list or a tuple, in
317the range of 0-255. An alpha
value of 255 (maximal opacity) will be assumed.
Red-green-blue-alpha components given
separately in either a comma-, slash- or
whitespace-separated string or a list or a tuple, in the

Functions

Module igraph.drawing.colors

hsla_to_rgba(h, s, l, alpha=1.0)
Converts a color given by its HSLA coordinates (hue, saturation, lightness,
alpha) to RGBA coordinates.
Each of the HSLA coordinates must be in the range [0, 1].
hsl_to_rgb(h, s, l )
Converts a color given by its HSL coordinates (hue, saturation, lightness) to
RGB coordinates.
Each of the HSL coordinates must be in the range [0, 1].
hsva_to_rgba(h, s, v, alpha=1.0)
Converts a color given by its HSVA coordinates (hue, saturation, value, alpha)
to RGB coordinates.
Each of the HSVA coordinates must be in the range [0, 1].
hsv_to_rgb(h, s, v )
Converts a color given by its HSV coordinates (hue, saturation, value) to RGB
coordinates.
Each of the HSV coordinates must be in the range [0, 1].
rgba_to_hsla(r, g, b, alpha=1.0)
Converts a color given by its RGBA coordinates to HSLA coordinates (hue,
saturation, lightness, alpha).
Each of the RGBA coordinates must be in the range [0, 1].
rgba_to_hsva(r, g, b, alpha=1.0)
Converts a color given by its RGBA coordinates to HSVA coordinates (hue,
saturation, value, alpha).
Each of the RGBA coordinates must be in the range [0, 1].
rgb_to_hsl(r, g, b)
Converts a color given by its RGB coordinates to HSL coordinates (hue,
saturation, lightness).
Each of the RGB coordinates must be in the range [0, 1].
318

Class Palette

Module igraph.drawing.colors

rgb_to_hsv(r, g, b)
Converts a color given by its RGB coordinates to HSV coordinates (hue,
saturation, value).
Each of the RGB coordinates must be in the range [0, 1].

12.2

Variables
Name
known_colors
palettes

12.3

Description
Value: {alice blue: (0.941176470588,
0.972549019608, 1.0, 1.0)...
Value: {gray: <GradientPalette with
256 colors>, heat: <Adva...

Class Palette

object
igraph.drawing.colors.Palette

Known Subclasses: igraph.drawing.colors.AdvancedGradientPalette, igraph.drawing.colors.Precalculated

igraph.drawing.colors.GradientPalette, igraph.drawing.colors.RainbowPalette
Base class of color palettes.
Color palettes are mappings that assign integers from the range 0..n-1 to colors (4-tuples).
n is called the size or length of the palette. igraph comes with a number of predefined
palettes, so this class is useful for you only if you want to define your own palette. This can
be done by subclassing this class and implementing the Palette._get method as necessary.
Palettes can also be used as lists or dicts, for the __getitem__ method is overridden properly
to call Palette.get.
12.3.1

Methods

__init__(self, n)
x.__init__(...) initializes x; see help(type(x)) for signature
Overrides: object.__init__ extit(inherited documentation)

319

Class Palette

Module igraph.drawing.colors

clear_cache(self )
Clears the result cache.
The return values of Palette.get are cached. Use this method to clear the
cache.
get(self, v )
Returns the given color from the palette.
Values are cached: if the specific value given has already been looked up, its
value will be returned from the cache instead of calculating it again. Use
Palette.clear_cache to clear the cache if necessary.
Parameters
v: the color to be retrieved. If it is an integer, it is passed to
Palette._get to be translated to an RGBA quadruplet.
Otherwise it is passed to color_name_to_rgb() to determine the
RGBA values.
Return Value
the color as an RGBA quadruplet
Note: you shouldnt override this method in subclasses, override _get instead.
If you override this method, lookups in the known_colors dict wont work, so
you wont be able to refer to colors by names or RGBA quadruplets, only by
integer indices. The caching functionality will disappear as well. However, feel
free to override this method if this is exactly the behaviour you want.
get_many(self, colors)
Returns multiple colors from the palette.
Values are cached: if the specific value given has already been looked upon, its
value will be returned from the cache instead of calculating it again. Use
Palette.clear_cache to clear the cache if necessary.
Parameters
colors: the list of colors to be retrieved. The palette class tries to
make an educated guess here: if it is not possible to
interpret the value you passed here as a list of colors, the
class will simply try to interpret it as a single color by
forwarding the value to Palette.get.
Return Value
the colors as a list of RGBA quadruplets. The result will be a list
even if you passed a single color index or color name.

320

Class Palette

Module igraph.drawing.colors

__getitem__(self, v )
Returns the given color from the palette.
Values are cached: if the specific value given has already been looked up, its
value will be returned from the cache instead of calculating it again. Use
Palette.clear_cache to clear the cache if necessary.
Parameters
v: the color to be retrieved. If it is an integer, it is passed to
Palette._get to be translated to an RGBA quadruplet.
Otherwise it is passed to color_name_to_rgb() to determine the
RGBA values.
Return Value
the color as an RGBA quadruplet
Note: you shouldnt override this method in subclasses, override _get instead.
If you override this method, lookups in the known_colors dict wont work, so
you wont be able to refer to colors by names or RGBA quadruplets, only by
integer indices. The caching functionality will disappear as well. However, feel
free to override this method if this is exactly the behaviour you want.
__len__(self )
Returns the number of colors in this palette
__plot__(self, context, bbox, palette, *args, **kwds)
Plots the colors of the palette on the given Cairo context
Supported keyword arguments are:
border_width: line width of the border shown around the palette. If zero
or negative, the border is turned off. Default is 1.
grid_width: line width of the grid that separates palette cells. If zero or
negative, the grid is turned off. The grid is also turned off if the size of a
cell is less than three times the given line width. Default is 0. Fractional
widths are also allowed.
orientation: the orientation of the palette. Must be one of the following
values: left-right, bottom-top, right-left or top-bottom. Possible
aliases: horizontal = left-right, vertical = bottom-top, lr =
left-right, rl = right-left, tb = top-bottom, bt = bottom-top.
The default is left-right.

321

Class GradientPalette

Module igraph.drawing.colors

__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __str__(),
__subclasshook__()
12.3.2

Properties

Name

Description
Returns the number of colors in this palette

length
Inherited from object
__class__

12.4

Class GradientPalette

object
igraph.drawing.colors.Palette
igraph.drawing.colors.GradientPalette
Base class for gradient palettes
Gradient palettes contain a gradient between two given colors.
Example:
>>>
>>>

pal = GradientPalette("red",
pal.get(0)

"blue",

(1.0, 0.0, 0.0, 1.0)

>>>

pal.get(2)

(0.5, 0.0, 0.5, 1.0)

>>>

pal.get(4)

(0.0, 0.0, 1.0, 1.0)

322

Class AdvancedGradientPalette

12.4.1

Module igraph.drawing.colors

Methods

init(self, color1, color2, n=256)

Creates a gradient palette.
Parameters
color1: the color where the gradient starts.
color2: the color where the gradient ends.
n:

the number of colors in the palette.

Overrides: object.__init__
Inherited from igraph.drawing.colors.Palette(Section 12.3)
__getitem__(), __len__(), __plot__(), __repr__(), clear_cache(), get(),
get_many()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __str__(),
__subclasshook__()
12.4.2

Properties

Name
Description
Inherited from igraph.drawing.colors.Palette (Section 12.3)
length
Inherited from object
__class__

12.5

Class AdvancedGradientPalette

object
igraph.drawing.colors.Palette
igraph.drawing.colors.AdvancedGradientPalette
Advanced gradient that consists of more than two base colors.
Example:
>>>

pal = AdvancedGradientPalette(["red",
323

"black", "blue"],

n=9)

Class AdvancedGradientPalette

>>>

Module igraph.drawing.colors

pal.get(2)

(0.5, 0.0, 0.0, 1.0)

>>>

pal.get(7)

(0.0, 0.0, 0.75, 1.0)

12.5.1

Methods

init(self, colors, indices=None, n=256)

Creates an advanced gradient palette
Parameters
colors: the colors in the gradient.
indices: the color indices belonging to the given colors. If None,
the colors are distributed equidistantly
n:

the total number of colors in the palette

Properties

Name
Description
Inherited from igraph.drawing.colors.Palette (Section 12.3)
length
Inherited from object
__class__

324

Class RainbowPalette

12.6

Module igraph.drawing.colors

Class RainbowPalette

object
igraph.drawing.colors.Palette
igraph.drawing.colors.RainbowPalette
A palette that varies the hue of the colors along a scale.
Colors in a rainbow palette all have the same saturation, value and alpha components, while
the hue is varied between two given extremes linearly. This palette has the advantage that
it wraps around nicely if the hue is varied between zero and one (which is the default).
Example:
>>>
>>>

pal = RainbowPalette(n=120)
pal.get(0)

(1.0, 0.0, 0.0, 1.0)

>>>

pal.get(20)

(1.0, 1.0, 0.0, 1.0)

>>>

pal.get(40)

(0.0, 1.0, 0.0, 1.0)

>>>
>>>

pal = RainbowPalette(n=120, s=1, v=0.5, alpha=0.75)

pal.get(60)

(0.0, 0.5, 0.5, 0.75)

>>>

pal.get(80)

(0.0, 0.0, 0.5, 0.75)

>>>

pal.get(100)

(0.5, 0.0, 0.5, 0.75)

>>>
>>>
>>>

pal = RainbowPalette(n=120)
pal2 = RainbowPalette(n=120, start=0.5, end=0.5)
pal.get(60) == pal2.get(0)

True
>>>

pal.get(90) == pal2.get(30)

True

This palette was modeled after the rainbow command of R.

325

Class PrecalculatedPalette

12.6.1

Module igraph.drawing.colors

Methods

init(self, n=256, s=1, v =1, start=0, end =1, alpha=1)

Creates a rainbow palette.
Parameters
n:
the number of colors in the palette.
s:

the saturation of the colors in the palette.

the value component of the colors in the palette.

start: the hue at which the rainbow begins (between 0 and 1).
end:

the hue at which the rainbow ends (between 0 and 1).

alpha: the alpha component of the colors in the palette.

Properties

Name
Description
Inherited from igraph.drawing.colors.Palette (Section 12.3)
length
Inherited from object
__class__

12.7

Class PrecalculatedPalette

object
igraph.drawing.colors.Palette
igraph.drawing.colors.PrecalculatedPalette

326

Class ClusterColoringPalette

Module igraph.drawing.colors

Known Subclasses: igraph.drawing.colors.ClusterColoringPalette

A palette that returns colors from a pre-calculated list of colors
12.7.1

Methods

__init__(self, l )
Creates the palette backed by the given list. The list must contain RGBA
quadruplets or color names, which will be resolved first by
color_name_to_rgba(). Anything that is understood by
color_name_to_rgba() is OK here.
Overrides: object.__init__
Inherited from igraph.drawing.colors.Palette(Section 12.3)
__getitem__(), __len__(), __plot__(), __repr__(), clear_cache(), get(),
get_many()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __str__(),
__subclasshook__()
12.7.2

Properties

Name
Description
Inherited from igraph.drawing.colors.Palette (Section 12.3)
length
Inherited from object
__class__

12.8

Class ClusterColoringPalette

object
igraph.drawing.colors.Palette
igraph.drawing.colors.PrecalculatedPalette
igraph.drawing.colors.ClusterColoringPalette

327

Class ClusterColoringPalette

Module igraph.drawing.colors

A palette suitable for coloring vertices when plotting a clustering.

This palette tries to make sure that the colors are easily distinguishable. This is achieved
by using a set of base colors and their lighter and darker variants, depending on the number
of elements in the palette.
When the desired size of the palette is less than or equal to the number of base colors
(denoted by n), only the bsae colors will be used. When the size of the palette is larger than
n but less than 2*n, the base colors and their lighter variants will be used. Between 2*n
and 3*n, the base colors and their lighter and darker variants will be used. Above 3*n, more
darker and lighter variants will be generated, but this makes the individual colors less and
less distinguishable.
12.8.1

Methods

__init__(self, n)
Creates the palette backed by the given list. The list must contain RGBA
quadruplets or color names, which will be resolved first by
color_name_to_rgba(). Anything that is understood by
color_name_to_rgba() is OK here.
Overrides: object.__init__ extit(inherited documentation)
Inherited from igraph.drawing.colors.Palette(Section 12.3)
__getitem__(), __len__(), __plot__(), __repr__(), clear_cache(), get(),
get_many()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __str__(),
__subclasshook__()
12.8.2

Properties

Name
Description
Inherited from igraph.drawing.colors.Palette (Section 12.3)
length
Inherited from object
__class__

328

Class CoordinateSystem

Module igraph.drawing.coord

Coordinate systems and related plotting routines

License: GPL
13.1

Variables
Name
__package__

13.2

Description
Value: igraph.drawing

Class CoordinateSystem

object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.baseclasses.AbstractCairoDrawer
igraph.drawing.coord.CoordinateSystem
Known Subclasses: igraph.drawing.coord.DescartesCoordinateSystem
Class implementing a coordinate system object.
Coordinate system objects are used when drawing plots which 2D or 3D coordinate system
axes. This is an abstract class which must be extended in order to use it. In general, youll
only need the documentation of this class if you intend to implement an own coordinate
system not present in igraph yet.
13.2.1

Methods

init(self, context, bbox )

Initializes the coordinate system.
Parameters
context: the context on which the coordinate system will be drawn.
bbox:

the bounding box that will contain the coordinate system.

Overrides: object.__init__

329

Class DescartesCoordinateSystem

Module igraph.drawing.coord

draw(self )
Draws the coordinate system.
This method must be overridden in derived classes.
Overrides: igraph.drawing.baseclasses.AbstractDrawer.draw
local_to_context(self, x, y)
Converts local coordinates to the context coordinate system (given by the
bounding box).
This method must be overridden in derived classes.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
13.2.2

Properties

Name
Description
Inherited from igraph.drawing.baseclasses.AbstractCairoDrawer (Section 11.3)
bbox
Inherited from object
__class__

13.3

Class DescartesCoordinateSystem

object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.baseclasses.AbstractCairoDrawer
igraph.drawing.coord.CoordinateSystem

igraph.drawing.coord.DescartesCoordinateS
Class implementing a 2D Descartes coordinate system object.

330

Class DescartesCoordinateSystem

13.3.1

Module igraph.drawing.coord

Methods

init(self, context, bbox, bounds)

Initializes the coordinate system.
Parameters
context: the context on which the coordinate system will be drawn.
bbox:

the bounding box that will contain the coordinate system.

bounds: minimum and maximum X and Y values in a 4-tuple.

Overrides: object.__init__
draw(self )
Draws the coordinate system.
Overrides: igraph.drawing.baseclasses.AbstractDrawer.draw
local_to_context(self, x, y)
Converts local coordinates to the context coordinate system (given by the
bounding box).
Overrides: igraph.drawing.coord.CoordinateSystem.local_to_context
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
13.3.2

Properties

Name
bbox
bounds

Description
Returns the bounding box of the coordinate
system
Returns the lower and upper bounds of the X
and Y values

Inherited from object

__class__

331

Module igraph.drawing.edge

Drawers for various edge styles in graph plots.

License: GPL
14.1

Class AbstractEdgeDrawer

object
igraph.drawing.edge.AbstractEdgeDrawer

Known Subclasses: igraph.drawing.edge.ArrowEdgeDrawer, igraph.drawing.edge.AlphaVaryingEdgeDra

igraph.drawing.edge.TaperedEdgeDrawer
Abstract edge drawer object from which all concrete edge drawer implementations are derived.
14.1.1

Methods

init(self, context, palette)

Constructs the edge drawer.
Parameters
context: a Cairo context on which the edges will be drawn.
palette: the palette that can be used to map integer color indices
to colors when drawing edges
Overrides: object.__init__
draw_directed_edge(self, edge, src_vertex, dest_vertex )
Draws a directed edge.
Parameters
edge:

the edge to be drawn. Visual properties of the edge

are defined by the attributes of this object.

src_vertex: the source vertex. Visual properties are given again

as attributes.
dest_vertex: the target vertex. Visual properties are given again
as attributes.

332

Class AbstractEdgeDrawer

Module igraph.drawing.edge

draw_loop_edge(self, edge, vertex )

Draws a loop edge.
The default implementation draws a small circle.
Parameters
edge: the edge to be drawn. Visual properties of the edge are
defined by the attributes of this object.
vertex: the vertex to which the edge is attached. Visual properties
are given again as attributes.
draw_undirected_edge(self, edge, src_vertex, dest_vertex )
Draws an undirected edge.
The default implementation of this method draws undirected edges as straight
lines. Loop edges are drawn as small circles.
Parameters
edge:

the edge to be drawn. Visual properties of the edge

are defined by the attributes of this object.

src_vertex: the source vertex. Visual properties are given again

as attributes.
dest_vertex: the target vertex. Visual properties are given again
as attributes.

333

Class ArrowEdgeDrawer

Module igraph.drawing.edge

get_label_position(self, edge, src_vertex, dest_vertex )

Returns the position where the label of an edge should be drawn. The default
implementation returns the midpoint of the edge and an alignment that tries
to avoid overlapping the label with the edge.
Parameters
edge:

the edge to be drawn. Visual properties of the edge

are defined by the attributes of this object.

src_vertex: the source vertex. Visual properties are given again

as attributes.
dest_vertex: the target vertex. Visual properties are given again
as attributes.
Return Value
a tuple containing two more tuples: the desired position of the label
and the desired alignment of the label, where the position is given as
(x, y) and the alignment is given as (horizontal, vertical).
Members of the alignment tuple are taken from constants in the
TextAlignment class.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
14.1.2

Properties

Name
Inherited from object
__class__

14.2

Description

Class ArrowEdgeDrawer

object
igraph.drawing.edge.AbstractEdgeDrawer
igraph.drawing.edge.ArrowEdgeDrawer
Edge drawer implementation that draws undirected edges as straight lines and directed edges
as arrows.

334

Class TaperedEdgeDrawer

14.2.1

Module igraph.drawing.edge

Methods

draw_directed_edge(self, edge, src_vertex, dest_vertex )

Draws a directed edge.
Parameters
edge:

the edge to be drawn. Visual properties of the edge

are defined by the attributes of this object.

src_vertex: the source vertex. Visual properties are given again

as attributes.
dest_vertex: the target vertex. Visual properties are given again
as attributes.
Overrides: igraph.drawing.edge.AbstractEdgeDrawer.draw_directed_edge
extit(inherited documentation)
Inherited from igraph.drawing.edge.AbstractEdgeDrawer(Section 14.1)
__init__(), draw_loop_edge(), draw_undirected_edge(), get_label_position()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
14.2.2

Properties

Name
Inherited from object
__class__

14.3

Description

Class TaperedEdgeDrawer

object
igraph.drawing.edge.AbstractEdgeDrawer
igraph.drawing.edge.TaperedEdgeDrawer
Edge drawer implementation that draws undirected edges as straight lines and directed edges
as tapered lines that are wider at the source and narrow at the destination.

335

Class AlphaVaryingEdgeDrawer

14.3.1

Module igraph.drawing.edge

Methods

draw_directed_edge(self, edge, src_vertex, dest_vertex )

Draws a directed edge.
Parameters
edge:

the edge to be drawn. Visual properties of the edge

are defined by the attributes of this object.

src_vertex: the source vertex. Visual properties are given again

Properties

Name
Inherited from object
__class__

14.4

Description

Class AlphaVaryingEdgeDrawer

object
igraph.drawing.edge.AbstractEdgeDrawer
igraph.drawing.edge.AlphaVaryingEdgeDrawer

Known Subclasses: igraph.drawing.edge.DarkToLightEdgeDrawer, igraph.drawing.edge.LightToDarkEd

Edge drawer implementation that draws undirected edges as straight lines and directed edges

336

Class AlphaVaryingEdgeDrawer

Module igraph.drawing.edge

by varying the alpha value of the specified edge color between the source and the destination.
14.4.1

Methods

init(self, context, alpha_at_src, alpha_at_dest)

Constructs the edge drawer.
Parameters
context: a Cairo context on which the edges will be drawn.
palette: the palette that can be used to map integer color indices
to colors when drawing edges
Overrides: object.__init__ extit(inherited documentation)
draw_directed_edge(self, edge, src_vertex, dest_vertex )
Draws a directed edge.
Parameters
edge:

the edge to be drawn. Visual properties of the edge

are defined by the attributes of this object.

src_vertex: the source vertex. Visual properties are given again

as attributes.
dest_vertex: the target vertex. Visual properties are given again
as attributes.
Overrides: igraph.drawing.edge.AbstractEdgeDrawer.draw_directed_edge
extit(inherited documentation)
Inherited from igraph.drawing.edge.AbstractEdgeDrawer(Section 14.1)
draw_loop_edge(), draw_undirected_edge(), get_label_position()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
14.4.2

Properties

Name
Inherited from object
__class__

Description

337

Class LightToDarkEdgeDrawer

14.5

Module igraph.drawing.edge

Class LightToDarkEdgeDrawer

object
igraph.drawing.edge.AbstractEdgeDrawer
igraph.drawing.edge.AlphaVaryingEdgeDrawer
igraph.drawing.edge.LightToDarkEdgeDrawer
Edge drawer implementation that draws undirected edges as straight lines and directed edges
by using an alpha value of zero (total transparency) at the source and an alpha value of one
(full opacity) at the destination. The alpha value is interpolated in-between.
14.5.1

Methods

__init__(self, context)
Constructs the edge drawer.
Parameters
context: a Cairo context on which the edges will be drawn.
palette: the palette that can be used to map integer color indices
to colors when drawing edges
Overrides: object.__init__ extit(inherited documentation)
Inherited from igraph.drawing.edge.AlphaVaryingEdgeDrawer(Section 14.4)
draw_directed_edge()
Inherited from igraph.drawing.edge.AbstractEdgeDrawer(Section 14.1)
draw_loop_edge(), draw_undirected_edge(), get_label_position()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
14.5.2

Properties

Name
Inherited from object
__class__

Description

338

Class DarkToLightEdgeDrawer

14.6

Module igraph.drawing.edge

Class DarkToLightEdgeDrawer

object
igraph.drawing.edge.AbstractEdgeDrawer
igraph.drawing.edge.AlphaVaryingEdgeDrawer
igraph.drawing.edge.DarkToLightEdgeDrawer
Edge drawer implementation that draws undirected edges as straight lines and directed edges
by using an alpha value of one (full opacity) at the source and an alpha value of zero (total
transparency) at the destination. The alpha value is interpolated in-between.
14.6.1

Methods

Properties

Name
Inherited from object
__class__

Description

339

Module igraph.drawing.graph

Drawing routines to draw graphs.

This module contains routines to draw graphs on:
Cairo surfaces (DefaultGraphDrawer)
UbiGraph displays (UbiGraphDrawer, see http://ubietylab.net/ubigraph)
It also contains routines to send an igraph graph directly to (Cytoscape6 ) using the (CytoscapeRPC plugin7 ), see CytoscapeGraphDrawer. CytoscapeGraphDrawer can also fetch
the current network from Cytoscape and convert it to igraph format.
License: GPL
15.1

Class DefaultGraphDrawer

340

Class DefaultGraphDrawer

15.1.1

Module igraph.drawing.graph

Methods

init(self, context, bbox, vertex_drawer_factory=<class

the context on which we will draw

the bounding box within which we will
draw. Can be anything accepted by the
constructor of BoundingBox (i.e., a
2-tuple, a 4-tuple or a BoundingBox
object).

vertex_drawer_factory: a factory method that returns an

a factory method that returns an

label_drawer_factory: a factory method that returns a

TextDrawer instance bound to a given
Cairo context. The method must take
one parameter: the Cairo context. The
default label drawer is TextDrawer.
Overrides: object.__init__

341

Class UbiGraphDrawer

Module igraph.drawing.graph

draw(self, graph, palette, *args, **kwds)

Properties

Name
Description
Inherited from igraph.drawing.baseclasses.AbstractCairoDrawer (Section 11.3)
bbox
Inherited from object
__class__

15.2

Class UbiGraphDrawer

object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.baseclasses.AbstractXMLRPCDrawer
object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.graph.AbstractGraphDrawer
igraph.drawing.graph.UbiGraphDrawer
Graph drawer that draws a given graph on an UbiGraph display using the XML-RPC API
of UbiGraph.
The following vertex attributes are supported: color, label, shape, size. See the Ubigraph
342

Class UbiGraphDrawer

Module igraph.drawing.graph

documentation for supported shape names. Sizes are relative to the default Ubigraph size.
The following edge attributes are supported: color, label, width. Edge widths are relative
to the default Ubigraph width.
All color specifications supported by igraph (e.g., color names, palette indices, RGB triplets,
RGBA quadruplets, HTML format) are understood by the Ubigraph graph drawer.
The drawer also has two attributes, vertex_defaults and edge_defaults. These are dictionaries that can be used to set default values for the vertex/edge attributes in Ubigraph.
15.2.1

Methods

init(self, url =http://localhost:20738/RPC2)

Constructs an UbiGraph drawer using the display at the given URL.
Parameters
url:

the URL where the XML-RPC calls for the service should
be addressed to.

service: the name of the service at the XML-RPC address. If

None, requests will be directed to the server proxy object
constructed by xmlrpclib.ServerProxy; if not None, the
given attribute will be looked up in the server proxy
object.
Overrides: object.__init__
draw(self, graph, *args, **kwds)
Draws the given graph on an UbiGraph display.
Parameters
clear: whether to clear the current UbiGraph display before
plotting. Default: True.
Overrides: igraph.drawing.baseclasses.AbstractDrawer.draw
Inherited from igraph.drawing.graph.AbstractGraphDrawer
ensure_layout()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()

343

Class CytoscapeGraphDrawer

15.2.2

Module igraph.drawing.graph

Properties

Name
Inherited from object
__class__

15.3

Description

Class CytoscapeGraphDrawer

object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.baseclasses.AbstractXMLRPCDrawer
object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.graph.AbstractGraphDrawer

igraph.drawing.graph.CytoscapeGraphDraw
Graph drawer that sends/receives graphs to/from Cytoscape using CytoscapeRPC.
This graph drawer cooperates with Cytoscape8 using CytoscapeRPC9 . You need to install
the CytoscapeRPC plugin first and start the XML-RPC server on a given port (port 9000
by default) from the appropriate Plugins submenu in Cytoscape.
Graph, vertex and edge attributes are transferred to Cytoscape whenever possible (i.e. when
a suitable mapping exists between a Python type and a Cytoscape type). If there is no
suitable Cytoscape type for a Python type, the drawer will use a string attribute on the
Cytoscape side and invoke str() on the Python attributes.
If an attribute to be created on the Cytoscape side already exists with a different type, an
underscore will be appended to the attribute name to resolve the type conflict.
You can use the network_id attribute of this class to figure out the network ID of the last
graph drawn with this drawer.
8 http://www.cytoscape.org
9 http://wiki.nbic.nl/index.php/CytoscapeRPC

344

Class CytoscapeGraphDrawer

15.3.1

Module igraph.drawing.graph

Methods

init(self, url =http://localhost:9000/Cytoscape)

Constructs a Cytoscape graph drawer using the XML-RPC interface of
Cytoscape at the given URL.
Parameters
url:

the URL where the XML-RPC calls for the service should
be addressed to.

service: the name of the service at the XML-RPC address. If

None, requests will be directed to the server proxy object
constructed by xmlrpclib.ServerProxy; if not None, the
given attribute will be looked up in the server proxy
object.
Overrides: object.__init__
draw(self, graph, name=Network from igraph, create_view =True, *args,
**kwds)
Sends the given graph to Cytoscape as a new network.
Parameters
name:

the name of the network in Cytoscape.

create_view: whether to create a view for the network in

Cytoscape.The default is True.
node_ids:

specifies the identifiers of the nodes to be used in

Cytoscape. This must either be the name of a vertex
attribute or a list specifying the identifiers, one for
each node in the graph. The default is None, which
simply uses the vertex index for each vertex.

Overrides: igraph.drawing.baseclasses.AbstractDrawer.draw

345

Class CytoscapeGraphDrawer

Module igraph.drawing.graph

fetch(self, name=None, directed =False, keep_canonical_names=False)

Fetches the network with the given name from Cytoscape.
When fetching networks from Cytoscape, the canonicalName attributes of
vertices and edges are not converted by default. Use the
keep_canonical_names parameter to retrieve these attributes as well.
Parameters
name:
directed:

the name of the network in Cytoscape.

whether the network is directed.

keep_canonical_names: whether to keep the canonicalName

vertex/edge attributes that are added
automatically by Cytoscape
Return Value
an appropriately constructed igraph Graph.
infer_cytoscape_type(values)
Returns a Cytoscape type that can be used to represent all the values in
values and an appropriately converted copy of values that is suitable for an
XML-RPC call. Note that the string type in Cytoscape is used as a catch-all
type; if no other type fits, attribute values will be converted to string and then
posted to Cytoscape.
None entries are allowed in values, they will be ignored on the Cytoscape
side.
Inherited from igraph.drawing.graph.AbstractGraphDrawer
ensure_layout()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
15.3.2

Properties

Name
Inherited from object
__class__

Description

346

Module igraph.drawing.metamagic

Auxiliary classes for the default graph drawer in igraph.

This module contains heavy metaclass magic. If you dont understand the logic behind these
classes, probably you dont need them either.
igraphs default graph drawer uses various data sources to determine the visual appearance
of vertices and edges. These data sources are the following (in order of precedence):
The keyword arguments passed to the igraph.plot() function (or to igraph.Graph.__plot__()
as a matter of fact, since igraph.plot() just passes these attributes on). For instance,
a keyword argument named vertex_label can be used to set the labels of vertices.
The attributes of the vertices/edges being drawn. For instance, a vertex that has a
label attribute will use that label when drawn by the default graph drawer.
The global configuration of igraph. For instance, if the global igraph.config.Configuration
instance has a key called plotting.vertex_color, that will be used as a default color
for the vertices.
If all else fails, there is a built-in default; for instance, the default vertex color is "red".
This is hard-wired in the source code.
The logic above can be useful in other graph drawers as well, not only in the default one,
therefore it is refactored into the classes found in this module. Different graph drawers may inspect different vertex or edge attributes, hence the classes that collect the attributes from the various data sources are generated in run-time using a metaclass called
AttributeCollectorMeta. You dont have to use AttributeCollectorMeta directly, just
implement a subclass of AttributeCollectorBase and it will ensure that the appropriate
metaclass is used. With AttributeCollectorBase, you can use a simple declarative syntax
to specify which attributes you are interested in. For example:
class VisualEdgeBuilder(AttributeCollectorBase):
arrow_size = 1.0
arrow_width = 1.0
color = ("black", palette.get)
width = 1.0
for edge in VisualEdgeBuilder(graph.es):
print edge.color
The above class is a visual edge builder a class that gives the visual attributes of the
edges of a graph that is specified at construction time. It specifies that the attributes we are
interested in are arrow_size, arrow_width, color and width; the default values are also
given. For color, we also specify that a method called {palette.get} should be called on
every attribute value to translate color names to RGB values. For the other three attributes,
float will implicitly be called on all attribute values, this is inferred from the type of the

347

Class AttributeSpecification

Module igraph.drawing.metamagic

default value itself.

See Also: AttributeCollectorMeta, AttributeCollectorBase
16.1

Class AttributeSpecification

object
igraph.drawing.metamagic.AttributeSpecification
Class that describes how the value of a given attribute should be retrieved.
The class contains the following members:
name: the name of the attribute. This is also used when we are trying to get its value
from a vertex/edge attribute of a graph.
alt_name: alternative name of the attribute. This is used when we are trying to
get its value from a Python dict or an igraph.Configuration object. If omitted at
construction time, it will be equal to name.
default: the default value of the attribute when none of the sources we try can provide
a meaningful value.
transform: optional transformation to be performed on the attribute value. If None or
omitted, it defaults to the type of the default value.
func: when given, this function will be called with an index in order to derive the value
of the attribute.
16.1.1

Methods

init(self, name, default=None, alt_name=None, transform=None,

func=None)
x.__init__(...) initializes x; see help(type(x)) for signature
Overrides: object.__init__ extit(inherited documentation)
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
16.1.2

Properties

348

Class AttributeCollectorBase

Module igraph.drawing.metamagic

Name
accessor
alt_name
default
func
name
transform
Inherited from object
__class__

16.2

Description

Class AttributeCollectorBase

object
igraph.drawing.metamagic.AttributeCollectorBase
Base class for attribute collector subclasses. Classes that inherit this class may use a
declarative syntax to specify which vertex or edge attributes they intend to collect. See
AttributeCollectorMeta for the details.
16.2.1

Methods

init(self, seq, kwds=None)

Constructs a new attribute collector that uses the given vertex/edge sequence
and the given dict as data sources.
Parameters
seq: an igraph.VertexSeq or igraph.EdgeSeq class that will be
used as a data source for attributes.
kwds: a Python dict that will be used to override the attributes
collected from seq if necessary.
Overrides: object.__init__
__getitem__(self, index )
Returns the collected attributes of the vertex/edge with the given index.
__len__(self )
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
349

Class AttributeCollectorBase

Module igraph.drawing.metamagic

reduce(), __reduce_ex(), repr(), setattr(), sizeof__(),

__str__(), __subclasshook__()
16.2.2

Properties

Name
Inherited from object
__class__

Description

350

Module igraph.drawing.shapes

Shape drawing classes for igraph

Vertex shapes in igraph are usually referred to by short names like "rect" or "circle". This
module contains the classes that implement the actual drawing routines for these shapes, and
a resolver class that determines the appropriate shape drawer class given the short name.
Classes that are derived from ShapeDrawer in this module are automatically registered by
ShapeDrawerDirectory. If you implement a custom shape drawer, you must register it in
ShapeDrawerDirectory manually if you wish to refer to it by a name in the shape attribute
of vertices.
License: Copyright (C) 2006-2012 Tams Nepusz <ntamas@gmail.com> Pzmny Pter
stny 1/a, 1117 Budapest, Hungary
This program is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation; either version
2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program;
if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
MA 02110-1301 USA
17.1

Class ShapeDrawerDirectory

object
igraph.drawing.shapes.ShapeDrawerDirectory
Static class that resolves shape names to their corresponding shape drawer classes.
Classes that are derived from ShapeDrawer in this module are automatically registered by
ShapeDrawerDirectory when the module is loaded for the first time.

351

Class ShapeDrawerDirectory

17.1.1

Module igraph.drawing.shapes

Methods

register(cls, drawer_class)
Registers the given shape drawer class under the given names.
Parameters
drawer_class: the shape drawer class to be registered
register_namespace(cls, namespace)
Registers all ShapeDrawer classes in the given namespace
Parameters
namespace: a Python dict mapping names to Python objects.
resolve(cls, shape)
Given a shape name, returns the corresponding shape drawer class
Parameters
shape: the name of the shape
Return Value
the corresponding shape drawer class
Raises
ValueError if the shape is unknown
resolve_default(cls, shape, default=<class
igraph.drawing.shapes.NullDrawer>)
Given a shape name, returns the corresponding shape drawer class or the
given default shape drawer if the shape name is unknown.
Parameters
shape:

the name of the shape

default: the default shape drawer to return when the shape is

unknown
Return Value
the shape drawer class corresponding to the given name or the
default shape drawer class if the name is unknown
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __init__(),
__new__(), __reduce__(), __reduce_ex__(), __repr__(), __setattr__(),
__sizeof__(), __str__(), __subclasshook__()

352

Class ShapeDrawerDirectory

17.1.2

Module igraph.drawing.shapes

Properties

Name
Inherited from object
__class__

17.1.3

Description

Class Variables

Name
known_shapes

Description
Value: {: <class
igraph.drawing.shapes.NullDrawer>,
arrow:...

353

Class TextAlignment

Module igraph.drawing.text

Drawers for labels on plots.

@undocumented: test License: GPL
18.1

Class TextAlignment

object
igraph.drawing.text.TextAlignment
Text alignment constants.
18.1.1

Methods

Inherited from object

__delattr__(), __format__(), __getattribute__(), __hash__(), __init__(),
__new__(), __reduce__(), __reduce_ex__(), __repr__(), __setattr__(),
__sizeof__(), __str__(), __subclasshook__()
18.1.2

Properties

Name
Inherited from object
__class__

18.1.3

Description

Class Variables

Name
BOTTOM
CENTER
LEFT
RIGHT
TOP

Value:
Value:
Value:
Value:
Value:

Description
bottom
center
left
right
top

354

Class TextDrawer

18.2

Module igraph.drawing.text

Class TextDrawer

object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.baseclasses.AbstractCairoDrawer
igraph.drawing.text.TextDrawer
Class that draws text on a Cairo context.
This class supports multi-line text unlike the original Cairo text drawing methods.
18.2.1

Methods

init(self, context, text=, halign=center, valign=center)

Constructs a new instance that will draw the given text on the given Cairo
context. Parameters
context: the context on which we will draw
bbox:

the bounding box within which we will draw. Can be

anything accepted by the constructor of BoundingBox
(i.e., a 2-tuple, a 4-tuple or a BoundingBox object).

Overrides: object.__init__
draw(self, wrap=False)

Draws the text in the current bounding box of the drawer.

Since the class itself is an instance of AbstractCairoDrawer, it has an
attribute named bbox which will be used as a bounding box. Parameters
wrap: whether to allow re-wrapping of the text if it does not fit
within the bounding box horizontally. (type=boolean)
Overrides: igraph.drawing.baseclasses.AbstractDrawer.draw

355

Class TextDrawer

Module igraph.drawing.text

get_text_layout(self, x =None, y=None, width=None, wrap=False)

Calculates the layout of the current text. x and y denote the coordinates
where the drawing should start. If they are both None, the current position of
the context will be used.
Vertical alignment settings are not taken into account in this method as the
text is not drawn within a box. Parameters
x:
The X coordinate of the reference point where the layout
should start. (type=float or None)
y:

The Y coordinate of the reference point where the layout

should start. (type=float or None)

width: The width of the box in which the text will be fitted. It
matters only when the text is right-aligned or centered. The
text will overflow the box if any of the lines is longer than
the box width and wrap is False. (type=float or None)
wrap: whether to allow re-wrapping of the text if it does not fit
within the given width. (type=boolean)
Return Value
a list consisting of (x, y, line) tuples where x and y refer to
reference points on the Cairo canvas and line refers to the
corresponding text that should be plotted there.

356

Class TextDrawer

Module igraph.drawing.text

draw_at(self, x =None, y=None, width=None, wrap=False)

Draws the text by setting up an appropriate path on the Cairo context and
filling it. x and y denote the coordinates where the drawing should start. If
they are both None, the current position of the context will be used.
Vertical alignment settings are not taken into account in this method as the
text is not drawn within a box. Parameters
x:
The X coordinate of the reference point where the drawing
should start. (type=float or None)
y:

The Y coordinate of the reference point where the drawing

should start. (type=float or None)

Returns the X-bearing, Y-bearing, width, height, X-advance and Y-advance of

the text.
For multi-line text, the X-bearing and Y-bearing correspond to the first line,
while the X-advance is extracted from the last line. and the Y-advance is the
sum of all the Y-advances. The width and height correspond to the entire
bounding box of the text.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
18.2.2

Properties

Name
Description
text
Returns the text to be drawn.
Inherited from igraph.drawing.baseclasses.AbstractCairoDrawer (Section 11.3)
bbox
continued on next page

357

Class TextDrawer

Module igraph.drawing.text

Name
Inherited from object
__class__

18.2.3

Description

Class Variables

Name
BOTTOM
CENTER
LEFT
RIGHT
TOP

Value:
Value:
Value:
Value:
Value:

Description
bottom
center
left
right
top

358

Module igraph.drawing.utils

Utility classes for drawing routines.

License: GPL
19.1

Class Rectangle

object
igraph.drawing.utils.Rectangle
Known Subclasses: igraph.drawing.utils.BoundingBox
Class representing a rectangle.
19.1.1

Methods

359

Class Rectangle

Module igraph.drawing.utils

isdisjoint(self, other )
Returns True if the two rectangles have no intersection.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1.isdisjoint(r2)
False
>>> r2.isdisjoint(r1)
False
>>> r1.isdisjoint(r3)
True
>>> r3.isdisjoint(r1)
True
isempty(self )
Returns True if the rectangle is empty (i.e. it has zero width and height).
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(70, 70, 90, 90)
>>> r1.isempty()
False
>>> r2.isempty()
False
>>> r1.intersection(r2).isempty()
True

360

Class Rectangle

Module igraph.drawing.utils

intersection(self, other )
Returns the intersection of this rectangle with another.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1.intersection(r2)
Rectangle(20.0, 20.0, 30.0, 30.0)
>>> r2 & r1
Rectangle(20.0, 20.0, 30.0, 30.0)
>>> r2.intersection(r1) == r1.intersection(r2)
True
>>> r1.intersection(r3)
Rectangle(0.0, 0.0, 0.0, 0.0)
__and__(self, other )
Returns the intersection of this rectangle with another.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1.intersection(r2)
Rectangle(20.0, 20.0, 30.0, 30.0)
>>> r2 & r1
Rectangle(20.0, 20.0, 30.0, 30.0)
>>> r2.intersection(r1) == r1.intersection(r2)
True
>>> r1.intersection(r3)
Rectangle(0.0, 0.0, 0.0, 0.0)

361

Class Rectangle

Module igraph.drawing.utils

translate(self, dx, dy)

Translates the rectangle in-place.
Example:
>>>
>>>
>>>

r = Rectangle(10, 20, 50, 70)

r.translate(30, -10)
r

Rectangle(40.0, 10.0, 80.0, 60.0)

Parameters
dx: the X coordinate of the translation vector
dy: the Y coordinate of the translation vector
union(self, other )
Returns the union of this rectangle with another.
The resulting rectangle is the smallest rectangle that contains both rectangles.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1.union(r2)
Rectangle(10.0, 10.0, 50.0, 50.0)
>>> r2 | r1
Rectangle(10.0, 10.0, 50.0, 50.0)
>>> r2.union(r1) == r1.union(r2)
True
>>> r1.union(r3)
Rectangle(10.0, 10.0, 90.0, 90.0)

362

Class Rectangle

Module igraph.drawing.utils

__or__(self, other )
Returns the union of this rectangle with another.
The resulting rectangle is the smallest rectangle that contains both rectangles.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1.union(r2)
Rectangle(10.0, 10.0, 50.0, 50.0)
>>> r2 | r1
Rectangle(10.0, 10.0, 50.0, 50.0)
>>> r2.union(r1) == r1.union(r2)
True
>>> r1.union(r3)
Rectangle(10.0, 10.0, 90.0, 90.0)
__ior__(self, other )
Expands this rectangle to include itself and another completely while still
being as small as possible.
Example:
>>> r1 = Rectangle(10, 10, 30, 30)
>>> r2 = Rectangle(20, 20, 50, 50)
>>> r3 = Rectangle(70, 70, 90, 90)
>>> r1 |= r2
>>> r1
Rectangle(10.0, 10.0, 50.0, 50.0)
>>> r1 |= r3
>>> r1
Rectangle(10.0, 10.0, 90.0, 90.0)
__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
__eq__(self, other )
__ne__(self, other )
363

Class BoundingBox

Module igraph.drawing.utils

__bool__(self )
__nonzero__(self )
__hash__(self )
hash(x)
Overrides: object.__hash__ extit(inherited documentation)
Inherited from object
__delattr__(), __format__(), __getattribute__(), __new__(), __reduce__(),
__reduce_ex__(), __setattr__(), __sizeof__(), __str__(), __subclasshook__()
19.1.2

Properties

Name
coords

width
height
left
right
top
bottom
midx
midy
shape
Inherited from object
__class__

19.2

Class BoundingBox

object
igraph.drawing.utils.Rectangle
igraph.drawing.utils.BoundingBox
Class representing a bounding box (a rectangular area) that encloses some objects.
364

Class BoundingBox

19.2.1

Module igraph.drawing.utils

Methods

Properties

Name
Description
Inherited from igraph.drawing.utils.Rectangle (Section 19.1)
bottom, coords, height, left, midx, midy, right, shape, top, width
Inherited from object
continued on next page

365

Class FakeModule

Module igraph.drawing.utils

Name
__class__

19.3

Description

Class FakeModule

object
igraph.drawing.utils.FakeModule
Fake module that raises an exception for everything
19.3.1

Methods

__getattr__(self, _)
__call__(self, _)
__setattr__(self, key, value)
x.__setattr__(name, value) <==> x.name = value
Overrides: object.__setattr__ extit(inherited documentation)
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __init__(),
__new__(), __reduce__(), __reduce_ex__(), __repr__(), __sizeof__(),
__str__(), __subclasshook__()
19.3.2

Properties

Name
Inherited from object
__class__

Description

366

Class Point

19.4

Module igraph.drawing.utils

Class Point

object
tuple
igraph.drawing.utils.Point
Class representing a point on the 2D plane.
19.4.1

Methods

367

Class Point

Module igraph.drawing.utils

__rmul__(self, scalar )
Multiplies the coordinates by a scalar
Overrides: tuple.__rmul__
__div__(self, scalar )
Divides the coordinates by a scalar
as_polar(self )
Returns the polar coordinate representation of the point.
Return Value
the radius and the angle in a tuple.
distance(self, other )
Returns the distance of the point from another one.
Example:
>>>
>>>
>>>

p1 = Point(5, 7)
p2 = Point(8, 3)
p1.distance(p2)

5.0

interpolate(self, other, ratio=0.5)

Linearly interpolates between the coordinates of this point and another one.
Parameters
other: the other point
ratio: the interpolation ratio between 0 and 1. Zero will return this
point, 1 will return the other point.
length(self )
Returns the length of the vector pointing from the origin to this point.
normalized(self )
Normalizes the coordinates of the point s.t. its length will be 1 after
normalization. Returns the normalized point.
sq_length(self )
Returns the squared length of the vector pointing from the origin to this point.
368

Class Point

Module igraph.drawing.utils

towards(self, other, distance=0)

Returns the point that is at a given distance from this point towards another
one.
FromPolar(cls, radius, angle)
Constructs a point from polar coordinates.
radius is the distance of the point from the origin; angle is the angle
between the X axis and the vector pointing to the point from the origin.
Inherited from tuple
__contains__(), __eq__(), __ge__(), __getattribute__(), __getitem__(),
__getslice__(), __gt__(), __hash__(), __iter__(), __le__(), __len__(),
__lt__(), __ne__(), __sizeof__(), count(), index()
Inherited from object
__delattr__(), __format__(), __init__(), __reduce__(), __reduce_ex__(),
__setattr__(), __str__(), __subclasshook__()
19.4.2

Properties

Name
x
y
Inherited from object
__class__

Description
Alias for field number 0
Alias for field number 1

369

Module igraph.drawing.vertex

Drawing routines to draw the vertices of graphs.

This module provides implementations of vertex drawers, i.e. drawers that the default graph
drawer will use to draw vertices.
License: GPL
20.1

Class AbstractVertexDrawer

object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.vertex.AbstractVertexDrawer
Known Subclasses: igraph.drawing.vertex.AbstractCairoVertexDrawer
Abstract vertex drawer object from which all concrete vertex drawer implementations are
derived.
20.1.1

Methods

init(self, palette, layout)

Constructs the vertex drawer and associates it to the given palette.
Parameters
palette: the palette that can be used to map integer color indices
to colors when drawing vertices
layout: the layout of the vertices in the graph being drawn
Overrides: object.__init__

370

Class AbstractCairoVertexDrawer

Module igraph.drawing.vertex

draw(self, visual_vertex, vertex, coords)

Draws the given vertex.
Parameters
visual_vertex: object specifying the visual properties of the
vertex. Its structure is defined by the
VisualVertexBuilder of the DefaultGraphDrawer;
see its source code.
vertex:

the raw igraph vertex being drawn

coords:

the X and Y coordinates of the vertex as specified

by the layout algorithm, scaled into the bounding
box.

Overrides: igraph.drawing.baseclasses.AbstractDrawer.draw
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
20.1.2

Properties

Name
Inherited from object
__class__

20.2

Description

Class AbstractCairoVertexDrawer

object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.vertex.AbstractVertexDrawer
object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.baseclasses.AbstractCairoDrawer

igraph.drawing.vertex.AbstractCairoVertexDra

371

Class AbstractCairoVertexDrawer

Module igraph.drawing.vertex

Known Subclasses: igraph.drawing.vertex.DefaultVertexDrawer

Abstract base class for vertex drawers that draw on a Cairo canvas.
20.2.1

Methods

init(self, context, bbox, palette, layout)

Constructs the vertex drawer and associates it to the given Cairo context and
the given BoundingBox.
Parameters
context: the context on which we will draw
bbox:

the bounding box within which we will draw. Can be

anything accepted by the constructor of BoundingBox
(i.e., a 2-tuple, a 4-tuple or a BoundingBox object).

palette: the palette that can be used to map integer color indices
to colors when drawing vertices
layout: the layout of the vertices in the graph being drawn
Overrides: object.__init__
Inherited from igraph.drawing.vertex.AbstractVertexDrawer(Section 20.1)
draw()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
20.2.2

Properties

Name
Description
Inherited from igraph.drawing.baseclasses.AbstractCairoDrawer (Section 11.3)
bbox
Inherited from object
__class__

372

Class DefaultVertexDrawer

20.3

Module igraph.drawing.vertex

Class DefaultVertexDrawer

object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.vertex.AbstractVertexDrawer
object
igraph.drawing.baseclasses.AbstractDrawer
igraph.drawing.baseclasses.AbstractCairoDrawer
igraph.drawing.vertex.AbstractCairoVertexDrawer

igraph.drawing.vertex.DefaultVertexDrawe
The default vertex drawer implementation of igraph.
20.3.1

Methods

init(self, context, bbox, palette, layout)

Constructs the vertex drawer and associates it to the given Cairo context and
the given BoundingBox.
Parameters
context: the context on which we will draw
bbox:

the bounding box within which we will draw. Can be

anything accepted by the constructor of BoundingBox
(i.e., a 2-tuple, a 4-tuple or a BoundingBox object).

373

Class DefaultVertexDrawer

Module igraph.drawing.vertex

draw(self, visual_vertex, vertex, coords)

the raw igraph vertex being drawn

coords:

the X and Y coordinates of the vertex as specified

by the layout algorithm, scaled into the bounding
box.

Overrides: igraph.drawing.baseclasses.AbstractDrawer.draw extit(inherited

documentation)
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
20.3.2

Properties

Name
Description
Inherited from igraph.drawing.baseclasses.AbstractCairoDrawer (Section 11.3)
bbox
Inherited from object
__class__

374

Class Layout

Module igraph.layout

Layout-related code in the IGraph library.

This package contains the implementation of the Layout object.
License: Copyright (C) 2006-2012 Tams Nepusz <ntamas@gmail.com> Pzmny Pter
stny 1/a, 1117 Budapest, Hungary
This program is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation; either version
2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program;
if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
MA 02110-1301 USA
21.1

Variables
Name
__package__

21.2

Description
Value: igraph

Class Layout

object
igraph.layout.Layout
Represents the layout of a graph.
A layout is practically a list of coordinates in an n-dimensional space. This class is generic
in the sense that it can store coordinates in any n-dimensional space.
Layout objects are not associated directly with a graph. This is deliberate: there were times
when I worked with almost identical copies of the same graph, the only difference was that
they had different colors assigned to the vertices. It was particularly convenient for me to
use the same layout for all of them, especially when I made figures for a paper. However,
igraph will of course refuse to draw a graph with a layout that has less coordinates than
the node count of the graph.
Layouts behave exactly like lists when they are accessed using the item index operator
375

Class Layout

Module igraph.layout

([...]). They can even be iterated through. Items returned by the index operator are only
copies of the coordinates, but the stored coordinates can be modified by directly assigning
to an index.
>>>
>>>
>>>

layout = Layout([(0, 1), (0, 2)])

coords = layout[1]
print coords

[0, 2]
>>>

coords = (0, 3)
layout[1]

>>> print
[0, 2]
>>>

layout[1] = coords
layout[1]

>>> print
[0, 3]

21.2.1

Methods

init(self, coords=None, dim=None)

Constructor.
Parameters
coords: the coordinates to be stored in the layout.
dim:

the number of dimensions. If None, the number of

dimensions is determined automatically from the length of
the first item of the coordinate list. If there are no entries
in the coordinate list, the default will be 2. Generally, this
should be given if the length of the coordinate list is zero,
otherwise it should be left as is.

Overrides: object.__init__
__len__(self )
__getitem__(self, idx )
__setitem__(self, idx, value)
__delitem__(self, idx )
__copy__(self )

376

Class Layout

Module igraph.layout

__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
append(self, value)
Appends a new point to the layout
mirror(self, dim)
Mirrors the layout along the given dimension(s)
Parameters
dim: the list of dimensions or a single dimension
rotate(self, angle, dim1 =0, dim2 =1, **kwds)
Rotates the layout by the given degrees on the plane defined by the given two
dimensions.
Parameters
angle: the angle of the rotation, specified in degrees.
dim1:

the first axis of the plane of the rotation.

dim2:

the second axis of the plane of the rotation.

origin: the origin of the rotation. If not specified, the origin will be
the origin of the coordinate system.
scale(self, *args, **kwds)
Scales the layout.
Scaling parameters can be provided either through the scale keyword
argument or through plain unnamed arguments. If a single integer or float is
given, it is interpreted as a uniform multiplier to be applied on all dimensions.
If it is a list or tuple, its length must be equal to the number of dimensions in
the layout, and each element must be an integer or float describing the scaling
coefficient in one of the dimensions.
Parameters
scale: scaling coefficients (integer, float, list or tuple)
origin: the origin of scaling (this point will stay in place).
Optional, defaults to the origin of the coordinate system
being used.

377

Class Layout

Module igraph.layout

translate(self, *args, **kwds)

Translates the layout.
The translation vector can be provided either through the v keyword argument
or through plain unnamed arguments. If unnamed arguments are used, the
vector can be supplied as a single list (or tuple) or just as a series of
arguments. In all cases, the translation vector must have the same number of
dimensions as the layout.
Parameters
v: the translation vector
to_radial(self, min_angle=100, max_angle=80, min_radius=0.0,
max_radius=1.0)
Converts a planar layout to a radial one
This method applies only to 2D layouts. The X coordinate of the layout is
transformed to an angle, with min(x) corresponding to the parameter called
min_angle and max(y) corresponding to max_angle. Angles are given in
degrees, zero degree corresponds to the direction pointing upwards. The Y
coordinate is interpreted as a radius, with min(y) belonging to the minimum
and max(y) to the maximum radius given in the arguments.
This is not a fully generic polar coordinate transformation, but it is fairly
useful in creating radial tree layouts from ordinary top-down ones (thats why
the Y coordinate belongs to the radius). It can also be used in conjunction
with the Fruchterman-Reingold layout algorithm via its miny and maxy
parameters (see Graph.layout_fruchterman_reingold) to produce radial
layouts where the radius belongs to some property of the vertices.
Parameters
min_angle: the angle corresponding to the minimum X value
max_angle: the angle corresponding to the maximum X value
min_radius: the radius corresponding to the minimum Y value
max_radius: the radius corresponding to the maximum Y value

378

Class Layout

Module igraph.layout

transform(self, function, *args, **kwds)

Performs an arbitrary transformation on the layout
Additional positional and keyword arguments are passed intact to the given
function.
Parameters
function: a function which receives the coordinates as a tuple and
returns the transformed tuple.
centroid(self )
Returns the centroid of the layout.
The centroid of the layout is the arithmetic mean of the points in the layout.
Return Value
the centroid as a list of floats
boundaries(self, border =0)
Returns the boundaries of the layout.
The boundaries are the minimum and maximum coordinates along all
dimensions.
Parameters
border: this value gets subtracted from the minimum bounds and
gets added to the maximum bounds before returning the
coordinates of the box. Defaults to zero.
Return Value
the minimum and maximum coordinates along all dimensions, in a
tuple containing two lists, one for the minimum coordinates, the
other one for the maximum.
Raises
ValueError if the layout contains no layout items

379

Class Layout

Module igraph.layout

bounding_box(self, border =0)

Returns the bounding box of the layout.
The bounding box of the layout is the smallest box enclosing all the points in
the layout.
Parameters
border: this value gets subtracted from the minimum bounds and
gets added to the maximum bounds before returning the
coordinates of the box. Defaults to zero.
Return Value
the coordinates of the lower left and the upper right corner of the
box. "Lower left" means the minimum coordinates and "upper
right" means the maximum. These are encapsulated in a
BoundingBox object.
center(self, *args, **kwds)
Centers the layout around the given point.
The point itself can be supplied as multiple unnamed arguments, as a simple
unnamed list or as a keyword argument. This operation moves the centroid of
the layout to the given point. If no point is supplied, defaults to the origin of
the coordinate system.
Parameters
p: the point where the centroid of the layout will be after the
operation.
copy(self )
Creates an exact copy of the layout.

380

Class Layout

Module igraph.layout

fit_into(self, bbox, keep_aspect_ratio=True)

Fits the layout into the given bounding box.
The layout will be modified in-place.
Parameters
bbox:

the bounding box in which to fit the layout. If

the dimension of the layout is d, it can either
be a d-tuple (defining the sizes of the box), a
2d-tuple (defining the coordinates of the top
left and the bottom right point of the box), or
a BoundingBox object (for 2D layouts only).

keep_aspect_ratio: whether to keep the aspect ratio of the

current layout. If False, the layout will be
rescaled to fit exactly into the bounding box.
If True, the original aspect ratio of the layout
will be kept and it will be centered within the
bounding box.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __str__(),
__subclasshook__()
21.2.2

Properties

Name
dim
coords
Inherited from object
__class__

Description
Returns the number of dimensions
The coordinates as a list of lists

381

Class Matching

Module igraph.matching

Classes representing matchings on graphs.

Variables
Name
__package__

22.2

Description
Value: igraph

Class Matching

object
igraph.matching.Matching
A matching of vertices in a graph.
A matching of an undirected graph is a set of edges such that each vertex is incident on
at most one matched edge. When each vertex is incident on exactly one matched edge, the
matching called perfect. This class is used in igraph to represent non-perfect and perfect
matchings in undirected graphs.
This class is usually not instantiated directly, everything is taken care of by the functions
that return matchings.
Examples:
igraph import Graph
g = Graph.Famous("noperfectmatching")
matching = g.maximum_matching()

>>> from
>>>
>>>

382

Class Matching

22.2.1

Module igraph.matching

Methods

init(self, graph, matching, types=None)

Initializes the matching.
Parameters
graph:

the graph the matching belongs to

matching: a numeric vector where element i corresponds to vertex i

of the graph. Element i is -1 or if the corresponding
vertex is unmatched, otherwise it contains the index of
the vertex to which vertex i is matched.
types:

the types of the vertices if the graph is bipartite. It must

either be the name of a vertex attribute (which will be
retrieved for all vertices) or a list. Elements in the list
will be converted to boolean values True or False, and
this will determine which part of the bipartite graph a
given vertex belongs to.

Raises
ValueError if the matching vector supplied does not describe a
valid matching of the graph.
Overrides: object.__init__
__len__(self )
__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
__str__(self )
str(x)
Overrides: object.__str__ extit(inherited documentation)
edges(self )
Returns an edge sequence that contains the edges in the matching.
If there are multiple edges between a pair of matched vertices, only one of
them will be returned.

383

Class Matching

Module igraph.matching

is_maximal(self )
Returns whether the matching is maximal.
A matching is maximal when it is not possible to extend it any more with
extra edges; in other words, unmatched vertices in the graph must be adjacent
to matched vertices only.
is_matched(self, vertex )
Returns whether the given vertex is matched to another one.
match_of (self, vertex )
Returns the vertex a given vertex is matched to.
Parameters
vertex: the vertex we are interested in; either an integer index or
an instance of Vertex.
Return Value
the index of the vertex matched to the given vertex, either as an
integer index (if vertex was integer) or as an instance of Vertex.
When the vertex is unmatched, returns None.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __subclasshook__()
22.2.2

Properties

Name
graph
matching

types

Description
Returns the graph corresponding to the
matching.
Returns the matching vector where element i
contains the ID of the vertex that vertex i is
matched to.
The matching vector will contain -1 for
unmatched vertices.
Returns the type vector if the graph is bipartite.
Element i of the type vector will be False or
True depending on which side of the bipartite
graph vertex i belongs to.
For non-bipartite graphs, this property returns
None.
continued on next page

384

Class Matching

Module igraph.matching

Name
Inherited from object
__class__

Description

385

Variables

Package igraph.remote

Classes that help igraph communicate with remote applications.

23.1

Modules

gephi: Classes that help igraph communicate with Gephi (http://www.gephi.org).

(Section 24, p. 381)
nexus: Interface to the Nexus online graph repository.
(Section 25, p. 388)
23.2

Variables
Name
__package__

Description
Value: None

386

Module igraph.remote.gephi

Classes that help igraph communicate with Gephi (http://www.gephi.org). License:

Copyright (C) 2006-2012 Tams Nepusz <ntamas@gmail.com> Pzmny Pter stny 1/a,
1117 Budapest, Hungary
This program is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation; either version
2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program;
if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
MA 02110-1301 USA
24.1

Class GephiConnection

object
igraph.remote.gephi.GephiConnection
Object that represents a connection to a Gephi master server.
24.1.1

Methods

init(self, url =None, host=127.0.0.1, port=8080, workspace=0)

Constructs a connection to a Gephi master server.

The connection object can be constructed either by specifying the url directly,
or by specifying the host, port and workspace arguments. The latter three
are evaluated only if url is None; otherwise the url will take precedence.
The url argument does not have to include the operation (e.g.,
?operation=updateGraph); the connection will take care of it. E.g., if you
wish to connect to workspace 2 in a local Gephi instance on port 7341, the
correct form to use for the url is as follows:
http://localhost:7341/workspace0
Overrides: object.__init__
387

Class GephiConnection

Module igraph.remote.gephi

__del__(self )
close(self )

Flushes all the pending operations to the Gephi master server in a single
request.
flush(self )

Flushes all the pending operations to the Gephi master server in a single
request.
write(self, data)

Sends the given raw data to the Gephi streaming master server in an HTTP
POST request.
__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __str__(),
__subclasshook__()
24.1.2

Properties

Name
url

Description
The URL of the Gephi workspace where the
data will be sent.

Inherited from object

__class__

388

Class GephiGraphStreamingAPIFormat

24.2

Module igraph.remote.gephi

Class GephiGraphStreamingAPIFormat

object
igraph.remote.gephi.GephiGraphStreamingAPIFormat
Object that implements the Gephi graph streaming API format and returns Python objects
corresponding to the events defined in the API.
24.2.1

Methods

get_add_node_event(self, identifier, attributes={})

Generates a Python object corresponding to the event that adds a node with
the given identifier and attributes in the Gephi graph streaming API.
Example:
>>> api = GephiGraphStreamingAPIFormat()
>>> api.get_add_node_event("spam")
{an: {spam: {}}}
>>> api.get_add_node_event("spam", dict(ham="eggs"))
{an: {spam: {ham: eggs}}}
get_add_edge_event(self, identifier, source, target, directed, attributes={})

Generates a Python object corresponding to the event that adds an edge with
the given source, target, directednessr and attributes in the Gephi graph
streaming API.

389

Class GephiGraphStreamingAPIFormat

Module igraph.remote.gephi

get_change_node_event(self, identifier, attributes)

Generates a Python object corresponding to the event that changes the

attributes of some node in the Gephi graph streaming API. The given
attributes are merged into the existing ones; use C{None} as the attribute
value to delete a given attribute.
Example:
>>> api = GephiGraphStreamingAPIFormat()
>>> api.get_change_node_event("spam", dict(ham="eggs"))
{cn: {spam: {ham: eggs}}}
>>> api.get_change_node_event("spam", dict(ham=None))
{cn: {spam: {ham: None}}}
get_change_edge_event(self, identifier, attributes)

Generates a Python object corresponding to the event that changes the

attributes of some edge in the Gephi graph streaming API. The given
attributes are merged into the existing ones; use C{None} as the attribute
value to delete a given attribute.
Example:
>>> api = GephiGraphStreamingAPIFormat()
>>> api.get_change_edge_event("spam", dict(ham="eggs"))
{ce: {spam: {ham: eggs}}}
>>> api.get_change_edge_event("spam", dict(ham=None))
{ce: {spam: {ham: None}}}
get_delete_node_event(self, identifier )

Generates a Python object corresponding to the event that deletes a node

with the given identifier in the Gephi graph streaming API.
Example:
>>> api = GephiGraphStreamingAPIFormat()
>>> api.get_delete_node_event("spam")
{dn: {spam: {}}}

390

Class GephiGraphStreamer

Module igraph.remote.gephi

get_delete_edge_event(self, identifier )

Generates a Python object corresponding to the event that deletes an edge

with the given identifier in the Gephi graph streaming API.
Example:
>>> api = GephiGraphStreamingAPIFormat()
>>> api.get_delete_edge_event("spam:ham")
{de: {spam:ham: {}}}
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __init__(),
__new__(), __reduce__(), __reduce_ex__(), __repr__(), __setattr__(),
__sizeof__(), __str__(), __subclasshook__()
24.2.2

Properties

Name
Inherited from object
__class__

24.3

Description

Class GephiGraphStreamer

object
igraph.remote.gephi.GephiGraphStreamer
Class that produces JSON event objects that stream an igraph graph to Gephi using the
Gephi Graph Streaming API.
The Gephi graph streaming format is a simple JSON-based format that can be used to post
mutations to a graph (i.e. node and edge additions, removals and updates) to a remote
component. For instance, one can open up Gephi (http://www.gephi.org}), install the
Gephi graph streaming plugin and then send a graph from igraph straight into the Gephi
window by using GephiGraphStreamer with the appropriate URL where Gephi is listening.
Example:
>>> from cStringIO import StringIO
>>> from igraph import Graph
>>> buf = StringIO()
391

Class GephiGraphStreamer

Module igraph.remote.gephi

>>> streamer = GephiGraphStreamer()

>>> graph = Graph.Formula("A --> B, B --> C")
>>> streamer.post(graph, buf)
>>> print buf.getvalue()
# doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
{"an": {"igraph:...:v:0": {"name": "A"}}}
{"an": {"igraph:...:v:1": {"name": "B"}}}
{"an": {"igraph:...:v:2": {"name": "C"}}}
{"ae": {"igraph:...:e:0:1": {...}}}
{"ae": {"igraph:...:e:1:2": {...}}}
<BLANKLINE>
24.3.1

Methods

init(self, encoder =None)

Constructs a Gephi graph streamer that will post graphs to a given file-like
object or a Gephi connection.
encoder must either be None or an instance of json.JSONEncoder and it must
contain the JSON encoder to be used when posting JSON objects. Overrides:
object.__init__
iterjsonobj(self, graph)

Iterates over the JSON objects that build up the graph using the Gephi graph
streaming API. The objects returned from this function are Python objects;
they must be formatted with json.dumps before sending them to the
destination.
post(self, graph, destination, encoder =None)

Posts the given graph to the destination of the streamer using the given JSON
encoder. When encoder is None, it falls back to the default JSON encoder of
the streamer in the encoder property.
destination must be a file-like object or an instance of GephiConnection.

392

Class GephiGraphStreamer

Module igraph.remote.gephi

send_event(self, event, destination, encoder =None, flush=True)

Sends a single JSON event to the given destination using the given JSON
encoder. When encoder is None, it falls back to the default JSON encoder of
the streamer in the encoder property.
destination must be a file-like object or an instance of GephiConnection.
The method flushes the destination after sending the event. If you want to
avoid this (e.g., because you are sending many events), set flush to False.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
24.3.2

Properties

Name
Inherited from object
__class__

Description

393

Class NexusConnection

Module igraph.remote.nexus

Interface to the Nexus online graph repository.

The classes in this file facilitate access to the Nexus online graph repository at http://nexus.igraph.org.
The main entry point of this package is the Nexus variable, which is an instance of NexusConnection.
Use NexusConnection.get to get a particular network from Nexus, NexusConnection.list
to list networks having a given set of tags, NexusConnection.search to search in the dataset
descriptions, or NexusConnection.info to show the info sheet of a dataset.
License: Copyright (C) 2006-2012 Tams Nepusz <ntamas@gmail.com> Pzmny Pter
stny 1/a, 1117 Budapest, Hungary
This program is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation; either version
2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program;
if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
MA 02110-1301 USA
25.1

Variables
Name
Nexus

25.2

Description
Value: NexusConnection()

Class NexusConnection

object
igraph.remote.nexus.NexusConnection
Connection to a remote Nexus server.
In most cases, you will not have to instantiate this object, just use the global Nexus variable which is an instance of NexusConnection and connects to the Nexus repository at
http://nexus.igraph.org.
Example:

394

Class NexusConnection

>>> print

Nexus.info("karate")

Module igraph.remote.nexus

#doctest:+ELLIPSIS

Nexus dataset karate (#1)

vertices/edges: 34/78
name: Zacharys karate club
tags: social network; undirected; weighted
...
>>>

karate = Nexus.get("karate")
igraph import summary
summary(karate)

>>> from
>>>

IGRAPH UNW- 34 78 -- Zacharys karate club network

+ attr: Author (g), Citation (g), name (g), Faction (v), id (v), name (v), weight (e)

25.2.1

Methods

init(self, nexus_url =None)

Constructs a connection to a remote Nexus server.
Parameters
nexus_url: the root URL of the remote server. Leave it at its
default value (None) unless you have set up your own
Nexus server and you want to connect to that. None
fetches the URL from igraphs configuration file or uses
the default URL if no URL is specified in the
configuration file.
Overrides: object.__init__

395

Class NexusConnection

Module igraph.remote.nexus

get(self, id )
Retrieves the dataset with the given ID from Nexus.
Dataset IDs are formatted as follows: the name of a dataset on its own means
that a single network should be returned if the dataset contains a single
network, or multiple networks should be returned if the dataset contains
multiple networks. When the name is followed by a dot and a network ID,
only a single network will be returned: the one that has the given network ID.
When the name is followed by a dot and a star, a dictionary mapping network
IDs to networks will be returned even if the original dataset contains a single
network only.
E.g., getting "karate" would return a single network since the Zachary karate
club dataset contains one network only. Getting "karate.*" on the other
hand would return a dictionary with one entry that contains the Zachary
karate club network.
Parameters
id: the ID of the dataset to retrieve.
Return Value
an instance of Graph (if a single graph has to be returned) or a
dictionary mapping network IDs to instances of Graph.
info(self, id )
Retrieves informations about the dataset with the given numeric or string ID
from Nexus.
Parameters
id: the numeric or string ID of the dataset to retrieve.
Return Value
an instance of NexusDatasetInfo.

396

Class NexusConnection

Module igraph.remote.nexus

list(self, tags=None, operator =or, order =date)

Retrieves a list of datasets matching a set of tags from Nexus.
Parameters
tags:

the tags the returned datasets should have. None

retrieves all the datasets, a single string retrieves
datasets having that given tag. Multiple tags may also
be specified as a list, tuple or any other iterable.

operator: when multiple tags are given, this argument specifies

whether the retrieved datasets should match all the tags
("and") or any of them ("or").
order:

the order of entries; it must be one of "date", "name" or

"popularity".

Return Value
a NexusDatasetInfoList object, which basically acts like a list and
yields NexusDatasetInfo objects. The list is populated lazily; i.e.
the requests will be fired only when needed.
search(self, query, order =date)
Retrieves a list of datasets matching a query string from Nexus.
Parameters
query: the query string. Searches are case insensitive and Nexus
searches for complete words only. The special word OR can
be used to find datasets that contain any of the given words
(instead of all of them). Exact phrases must be enclosed in
quotes in the search string. See the Nexus webpage for more
information at http://nexus.igraph.org/web/docs#searching.
order: the order of entries; it must be one of "date", "name" or
"popularity".
Return Value
a NexusDatasetInfoList object, which basically acts like a list and
yields NexusDatasetInfo objects. The list is populated lazily; i.e.
the requests will be fired only when needed.
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__str__(), __subclasshook__()
25.2.2

Properties

397

Class NexusConnection

Name
url

Module igraph.remote.nexus

Description
Returns the root URL of the Nexus repository
the connection is communicating with.

Inherited from object

__class__

398

Module igraph.statistics

Statistics related stuff in igraph

License: Copyright (C) 2006-2012 Tamas Nepusz <ntamas@gmail.com> Pzmny Pter
stny 1/a, 1117 Budapest, Hungary
This program is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation; either version
2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program;
if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
MA 02110-1301 USA
26.1

Functions
mean(xs)
Returns the mean of an iterable.
Example:
>>>

mean([1, 4, 7, 11])

5.75

Parameters
xs: an iterable yielding numbers.
Return Value
the mean of the numbers provided by the iterable.
See Also: RunningMean() if you also need the variance or the standard
deviation

399

Functions

Module igraph.statistics

median(xs, sort=True)
Returns the median of an unsorted or sorted numeric vector.
Parameters
xs: the vector itself.
sort: whether to sort the vector. If you know that the vector is
sorted already, pass False here.
Return Value
the median, which will always be a float, even if the vector contained
integers originally.
percentile(xs, p=(25, 50, 75), sort=True)
Returns the pth percentile of an unsorted or sorted numeric vector.
This is equivalent to calling quantile(xs, p/100.0); see quantile for more
details on the calculation.
Example:
>>>

round(percentile([15, 20, 40, 35, 50], 40), 2)

26.0
>>> for
...

perc
print

percentile([15, 20, 40, 35, 50], (0, 25, 50, 75, 100)):
"%.2f" % perc

...
15.00
17.50
35.00
45.00
50.00

Parameters
xs: the vector itself.
p:

the percentile we are looking for. It may also be a list if you

want to calculate multiple quantiles with a single call. The
default value calculates the 25th, 50th and 75th percentile.

sort: whether to sort the vector. If you know that the vector is
sorted already, pass False here.
Return Value
the pth percentile, which will always be a float, even if the vector
contained integers originally. If p is a list, the result will also be a
list containing the percentiles for each item in the list.

400

Functions

Module igraph.statistics

power_law_fit(data, xmin=None, method =auto,

return_alpha_only=False)
Fitting a power-law distribution to empirical data
Parameters
data: the data to fit, a list containing integer values
xmin:

the lower bound for fitting the power-law. If None, the

optimal xmin value will be estimated as well. Zero means
that the smallest possible xmin value will be used.

method: the fitting method to use. The following methods are

implemented so far:
continuous, hill: exact maximum likelihood
estimation when the input data comes from a
continuous scale. This is known as the Hill estimator.
The statistical error of this estimator is (alpha-1) /
sqrt(n), where alpha is the estimated exponent and n is
the number of data points above xmin. The estimator is
known to exhibit a small finite sample-size bias of order
O(n^-1), which is small when n > 100. igraph will try
to compensate for the finite sample size if n is small.
discrete: exact maximum likelihood estimation when
the input comes from a discrete scale (see Clauset et al
among the references).
auto: exact maximum likelihood estimation where the
continuous method is used if the input vector contains
at least one fractional value and the discrete method is
used if the input vector contains integers only.
Return Value
a FittedPowerLaw object. The fitted xmin value and the power-law
exponent can be queried from the xmin and alpha properties of the
returned object.
Reference:
MEJ Newman: Power laws, Pareto distributions and Zipfs law.
Contemporary Physics 46, 323-351 (2005)
A Clauset, CR Shalizi, MEJ Newman: Power-law distributions
in empirical data. E-print (2007). arXiv:0706.1062

401

Class FittedPowerLaw

Module igraph.statistics

quantile(xs, q=(0.25, 0.5, 0.75), sort=True)

Returns the qth quantile of an unsorted or sorted numeric vector.
There are a number of different ways to calculate the sample quantile. The
method implemented by igraph is the one recommended by NIST. First we
calculate a rank n as q(N+1), where N is the number of items in xs, then we
split n into its integer component k and decimal component d. If k <= 1, we
return the first element; if k >= N, we return the last element, otherwise we
return the linear interpolation between xs[k-1] and xs[k] using a factor d.
Example:
>>>

round(quantile([15, 20, 40, 35, 50], 0.4), 2)

26.0

Parameters
xs: the vector itself.
the quantile we are looking for. It may also be a list if you
want to calculate multiple quantiles with a single call. The
default value calculates the 25th, 50th and 75th percentile.

sort: whether to sort the vector. If you know that the vector is
sorted already, pass False here.
Return Value
the qth quantile, which will always be a float, even if the vector
contained integers originally. If q is a list, the result will also be a
list containing the quantiles for each item in the list.
26.2

Class FittedPowerLaw

object
igraph.statistics.FittedPowerLaw
Result of fitting a power-law to a vector of samples
Example:
>>>
>>>

result = power_law_fit([1, 2, 3, 4, 5, 6])

result
# doctest:+ELLIPSIS

FittedPowerLaw(continuous=False, alpha=2.425828..., xmin=3.0, L=-7.54633..., D=0.2138..., p=0.99311...)

>>> print

result

# doctest:+ELLIPSIS

Fitted power-law distribution on discrete data

<BLANKLINE>
Exponent (alpha)

= 2.425828

402

Class FittedPowerLaw

Cutoff (xmin)

Module igraph.statistics

= 3.000000

<BLANKLINE>
Log-likelihood

= -7.546337

<BLANKLINE>
H0: data was drawn from the fitted distribution
<BLANKLINE>
KS test statistic = 0.213817
p-value

= 0.993111

<BLANKLINE>
H0 could not be rejected at significance level 0.05
>>>

result.alpha

# doctest:+ELLIPSIS

2.425828...
>>>

result.xmin

3.0
>>>

result.continuous

False

26.2.1

Methods

init(self, continuous, alpha, xmin, L, D, p)

x.__init__(...) initializes x; see help(type(x)) for signature
Overrides: object.__init__ extit(inherited documentation)
__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
__str__(self )
str(x)
Overrides: object.__str__ extit(inherited documentation)

403

Class Histogram

Module igraph.statistics

summary(self, significance=0.05)
Returns the summary of the power law fit.
Parameters
significance: the significance level of the Kolmogorov-Smirnov
test used to decide whether the input data could
have come from the fitted distribution
Return Value
the summary as a string
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __subclasshook__()
26.2.2

Properties

Name
Inherited from object
__class__

26.3

Description

Class Histogram

object
igraph.statistics.Histogram
Generic histogram class for real numbers
Example:
>>>
>>>
>>>

h = Histogram(5)
# Initializing, bin width = 5
h << [2,3,2,7,8,5,5,0,7,9]
# Adding more items
print h

N = 10, mean +- sd: 4.8000 +- 2.9740

[ 0,

5): **** (4)

[ 5, 10): ****** (6)

404

Class Histogram

26.3.1

Module igraph.statistics

Methods

init(self, bin_width=1, data=None)

Initializes the histogram with the given data set.
Parameters
bin_width: the bin width of the histogram.
data:

the data set to be used. Must contain real numbers.

Overrides: object.__init__
add(self, num, repeat=1)
Adds a single number to the histogram.
Parameters
num:
the number to be added
repeat: number of repeated additions
add_many(self, data)
Adds a single number or the elements of an iterable to the histogram.
Parameters
data: the data to be added
__lshift__(self, data)
Adds a single number or the elements of an iterable to the histogram.
Parameters
data: the data to be added
clear(self )
Clears the collected data
bins(self )
Generator returning the bins of the histogram in increasing order
Return Value
a tuple with the following elements: left bound, right bound, number
of elements in the bin
__plot__(self, context, bbox, _, **kwds)
Plotting support

405

Class Histogram

Module igraph.statistics

to_string(self, max_width=78, show_bars=True, show_counts=True)

Returns the string representation of the histogram.
Parameters
max_width:
show_bars:

the maximal width of each line of the string This

value may not be obeyed if it is too small.
specify whether the histogram bars should be shown

show_counts: specify whether the histogram counts should be

shown. If both show_bars and show_counts are
False, only a general descriptive statistics (number
of elements, mean and standard deviation) is shown.
__str__(self )
str(x)
Overrides: object.__str__ extit(inherited documentation)
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __repr__(), __setattr__(), __sizeof__(),
__subclasshook__()
26.3.2

Properties

Name
n
mean
sd
var

Description
Returns the number of elements in the
histogram
Returns the mean of the elements in the
histogram
Returns the standard deviation of the elements
in the histogram
Returns the variance of the elements in the
histogram

Inherited from object

__class__

406

Class RunningMean

26.4

Module igraph.statistics

Class RunningMean

object
igraph.statistics.RunningMean
Running mean calculator.
This class can be used to calculate the mean of elements from a list, tuple, iterable or any
other data source. The mean is calculated on the fly without explicitly summing the values,
so it can be used for data sets with arbitrary item count. Also capable of returning the
standard deviation (also calculated on the fly)
26.4.1

Methods

init(items=None, n=0.0, mean=0.0, sd =0.0)

Initializes the running mean calculator.
There are two possible ways to initialize the calculator. First, one can provide
an iterable of items; alternatively, one can specify the number of items, the
mean and the standard deviation if we want to continue an interrupted
calculation.
Parameters
items: the items that are used to initialize the running mean
calcuator. If items is given, n, mean and sd must be zeros.
n:

the initial number of elements already processed. If this is

given, items must be None.

mean: the initial mean. If this is given, items must be None.

sd:

the initial standard deviation. If this is given, items must

be None.

Overrides: object.__init__
add(RunningMean, value, repeat=1)
Adds the given value to the elements from which we calculate the mean and
the standard deviation.
Parameters
value: the element to be added
repeat: number of repeated additions

407

Class RunningMean

Module igraph.statistics

add_many(RunningMean, values)
Adds the values in the given iterable to the elements from which we calculate
the mean. Can also accept a single number. The left shift (<<) operator is
aliased to this function, so you can use it to add elements as well:
>>>
>>>
>>>

rm=RunningMean()
rm << [1,2,3,4]
rm.result

# doctest:+ELLIPSIS

(2.5, 1.290994...)

Parameters
values: the element(s) to be added
(type=iterable)
clear(self )
Resets the running mean calculator.
__repr__(self )
repr(x)
Overrides: object.__repr__ extit(inherited documentation)
__str__(self )
str(x)
Overrides: object.__str__ extit(inherited documentation)
__lshift__(RunningMean, values)
Adds the values in the given iterable to the elements from which we calculate
the mean. Can also accept a single number. The left shift (<<) operator is
aliased to this function, so you can use it to add elements as well:
>>>
>>>
>>>

rm=RunningMean()
rm << [1,2,3,4]
rm.result

# doctest:+ELLIPSIS

(2.5, 1.290994...)

Parameters
values: the element(s) to be added
(type=iterable)
__float__(self )
408

Class RunningMean

Module igraph.statistics

__int__(self )
__long__(self )
__complex__(self )
__len__(self )
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
__reduce__(), __reduce_ex__(), __setattr__(), __sizeof__(), __subclasshook__()
26.4.2

Properties

Name
result
mean
sd
var
Inherited from object
__class__

Description
Returns the current mean and standard
deviation as a tuple
Returns the current mean
Returns the current standard deviation
Returns the current variation

409

Module igraph.summary

Summary representation of a graph.

Class GraphSummary

object
igraph.summary.GraphSummary
Summary representation of a graph.
The summary representation includes a header line and the list of edges. The header line
consists of IGRAPH, followed by a four-character long code, the number of vertices, the number
of edges, two dashes () and the name of the graph (i.e. the contents of the name attribute,
if any). For instance, a header line may look like this:
IGRAPH U--- 4 5 -The four-character code describes some basic properties of the graph. The first character is
U if the graph is undirected, D if it is directed. The second letter is N if the graph has a vertex
attribute called name, or a dash otherwise. The third letter is W if the graph is weighted (i.e.
it has an edge attribute called weight), or a dash otherwise. The fourth letter is B if the
graph has a vertex attribute called type; this is usually used for bipartite graphs.
Edges may be presented as an ordinary edge list or an adjacency list. By default, this
depends on the number of edges; however, you can control it with the appropriate constructor
arguments.

410

Class GraphSummary

27.1.1

Module igraph.summary

Methods

init(self, graph, verbosity=0, width=78, edge_list_format=auto,

max_rows=99999, print_graph_attributes=False,
print_vertex_attributes=False, print_edge_attributes=False, full =False)
Constructs a summary representation of a graph.
Parameters
verbosity:

the verbosity of the summary. If zero,

only the header line will be returned.
If one, the header line and the list of
edges will both be returned.

width:

the maximal width of each line in the

summary. None means that no limit
will be enforced.

max_rows:

the maximal number of rows to print

in a single table (e.g., vertex attribute
table or edge attribute table)

edge_list_format:

format of the edge list in the summary.

Supported formats are: compressed,
adjlist, edgelist, auto, which
selects automatically from the other
three based on some simple criteria.

print_graph_attributes: whether to print graph attributes if

there are any.
print_vertex_attributes: whether to print vertex attributes if
there are any.
print_edge_attributes:

whether to print edge attributes if

there are any.

full:

False has no effect; True turns on the

attribute printing for graph, vertex
and edge attributes with verbosity 1.

Overrides: object.__init__
__str__(self )
Returns the summary representation as a string.
Overrides: object.__str__
Inherited from object
__delattr__(), __format__(), __getattribute__(), __hash__(), __new__(),
411

Class GraphSummary

Module igraph.summary

reduce(), __reduce_ex(), repr(), setattr(), sizeof__(),

__subclasshook__()
27.1.2

Properties

Name
Inherited from object
__class__

Description

412

Module igraph.utils

Utility functions that cannot be categorised anywhere else License: Copyright (C) 2006-2012
Tams Nepusz <ntamas@gmail.com> Pzmny Pter stny 1/a, 1117 Budapest, Hungary
This program is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation; either version
2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program;
if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
MA 02110-1301 USA
28.1

Functions
named_temporary_file(*args, **kwds)

Context manager that creates a named temporary file and returns its name.
All parameters are passed on to tempfile.mkstemp, see its documentation for
more info.

413

Functions

Module igraph.utils

rescale(values, out_range=(0.0, 1.0), in_range=None, clamp=False,

scale=None)

Rescales a list of numbers into a given range.

out_range gives the range of the output values; by default, the minimum of
the original numbers in the list will be mapped to the first element in the
output range and the maximum will be mapped to the second element.
Elements between the minimum and maximum values in the input list will be
interpolated linearly between the first and second values of the output range.
in_range may be used to override which numbers are mapped to the first and
second values of the output range. This must also be a tuple, where the first
element will be mapped to the first element of the output range and the
second element to the second.
If clamp is True, elements which are outside the given out_range after
rescaling are clamped to the output range to ensure that no number will be
outside out_range in the result.
If scale is not None, it will be called for every element of values and the
rescaling will take place on the results instead. This can be used, for instance,
to transform the logarithm of the original values instead of the actual values.
A typical use-case is to map a range of values to color identifiers on a
logarithmic scale. Scaling also applies to the in_range parameter if present.
Examples:
>>>

rescale(range(5), (0, 8))

[0.0, 2.0, 4.0, 6.0, 8.0]

>>>

rescale(range(5), (2, 10))

[2.0, 4.0, 6.0, 8.0, 10.0]

>>>

rescale(range(5), (0, 4), (1, 3))

[-2.0, 0.0, 2.0, 4.0, 6.0]

>>>

rescale(range(5), (0, 4), (1, 3), clamp=True)

[0.0, 0.0, 2.0, 4.0, 4.0]

>>>

rescale([0]*5, (1, 3))

[2.0, 2.0, 2.0, 2.0, 2.0]

math import log10

rescale([1, 10, 100, 1000, 10000], (0, 8), scale=log10)

>>> from
>>>

[0.0, 2.0, 4.0, 6.0, 8.0]

>>>

rescale([1, 10, 100, 1000, 10000], (0, 4), (10, 1000), scale=log10)

[-2.0, 0.0, 2.0, 4.0, 6.0]

414

Variables

Module igraph.utils

safemax(iterable, default=0)

Safer variant of max() that returns a default value if the iterable is empty.
Example:
>>>

safemax([-5, 6, 4])

6
>>>

safemax([])

0
>>>

safemax((), 2)

safemin(iterable, default=0)

Safer variant of min() that returns a default value if the iterable is empty.
Example:
>>>

safemin([-5, 6, 4])

-5
>>>

safemin([])

0
>>>

safemin((), 2)

28.2

Variables
Name
dbl_epsilon

Description
Value: 2.22044604925e-16

415

Class multidict

28.3

Module igraph.utils

Class multidict

object
_abcoll.Sized
object
_abcoll.Iterable
object
_abcoll.Container
_abcoll.Mapping
_abcoll.MutableMapping
igraph.utils.multidict
A dictionary-like object that is customized to deal with multiple values for the same key.
Each value in this dictionary will be a list. Methods which emulate the methods of a standard
Python dict object will return or manipulate the first items of the lists only. Special methods
are provided to deal with keys having multiple values.
28.3.1

Methods

init(self, *args, **kwds)

x.__init__(...) initializes x; see help(type(x)) for signature
Overrides: object.__init__ extit(inherited documentation)
__contains__(self, key)

Returns whether there are any items associated to the given key. Overrides:
_abcoll.Container.__contains__

416

Class multidict

Module igraph.utils

__delitem__(self, key)

Removes all the items associated to the given key. Overrides:

_abcoll.MutableMapping.__delitem__
__getitem__(self, key)

Returns an arbitrary item associated to the given key. Raises KeyError if no

such key exists.
Example:
>>>
>>>

d = multidict([("spam",
d["spam"]

"eggs"),

("spam",

"bacon")])

eggs

Overrides: _abcoll.Mapping.__getitem__
__iter__(self )

Iterates over the keys of the multidict. Overrides: _abcoll.Iterable.iter

__len__(self )

Returns the number of distinct keys in this multidict. Overrides:

_abcoll.Sized.__len__

417

Class multidict

Module igraph.utils

setitem(self, key, value)

Sets the item associated to the given key. Any values associated to the key
will be erased and replaced by value.
Example:
>>>
>>>
>>>

d = multidict([("spam",
d["spam"] = "ham"
d["spam"]

"eggs"),

("spam",

"bacon")])

ham

Overrides: _abcoll.MutableMapping.__setitem__
add(self, key, value)

Adds value to the list of items associated to key.

Example:
>>>
>>>
>>>

d = multidict()
d.add("spam", "ham")
d["spam"]

ham
>>>
>>>

d.add("spam", "eggs")
d.getlist("spam")

[ham, eggs]

clear(self )

Removes all the items from the multidict. Return Value

None
Overrides: _abcoll.MutableMapping.clear

418

Class multidict

Module igraph.utils

get(self, key, default=None)

Returns an arbitrary item associated to the given key. If key does not exist or
has zero associated items, default will be returned. Return Value
D[k] if k in D, else d
Overrides: _abcoll.Mapping.get
getlist(self, key)

Returns the list of values for the given key. An empty list will be returned if
there is no such key.
iterlists(self )

Iterates over (key, values) pairs where values is the list of values
associated with key.
lists(self )

Returns a list of (key, values) pairs where values is the list of values
associated with key.
update(self, arg, **kwds)
Update D from mapping/iterable E and F. If E present and has a .keys()
method, does: for k in E: D[k] = E[k] If E present and lacks .keys() method,
does: for (k, v) in E: D[k] = v In either case, this is followed by: for k, v in
F.items(): D[k] = v
Return Value
None
Overrides: _abcoll.MutableMapping.update extit(inherited documentation)
Inherited from _abcoll.MutableMapping
pop(), popitem(), setdefault()
Inherited from _abcoll.Mapping
__eq__(), __ne__(), items(), iteritems(), iterkeys(), itervalues(), keys(), val419

Class multidict

Module igraph.utils

ues()
Inherited from _abcoll.Sized
__subclasshook__()
Inherited from object
__delattr__(), __format__(), __getattribute__(), __new__(), __reduce__(),
__reduce_ex__(), __repr__(), __setattr__(), __sizeof__(), __str__()
28.3.2

Properties

Name
Inherited from object
__class__

28.3.3

Description

Class Variables

Name
Description
__abstractmethods__
Value: frozenset([])
Inherited from _abcoll.Mapping
__hash__

420

Index
igraph.configuration (module), 261266
igraph (package), 2215
igraph._igraph (module), 216220
igraph.configuration.Configuration (class),
igraph._igraph.convex_hull (function),
262266
216
igraph.configuration.get_platform_image_viewer
igraph._igraph.InternalError (class), 219
(function), 261
220
igraph.configuration.get_user_config_file
igraph._igraph.is_degree_sequence (func(function), 261
tion), 216
igraph.configuration.init (function), 261
igraph._igraph.is_graphical_degree_sequence
igraph.cut (module), 267273
(function), 217
igraph.cut.Cut (class), 267270
igraph._igraph.set_progress_handler (funcigraph.cut.Flow (class), 270273
igraph.datatypes (module), 274285
tion), 217
igraph._igraph.set_random_number_generator
igraph.datatypes.DyadCensus (class), 279
(function), 218
281
igraph._igraph.set_status_handler (funcigraph.datatypes.Matrix (class), 274279
tion), 218
igraph.datatypes.TriadCensus (class), 281
igraph.app (package), 221
283
igraph.app.shell (module), 222231
igraph.datatypes.UniqueIdGenerator (class),
igraph.ARPACKOptions (class), 9799
283285
igraph.autocurve (function), 4
igraph.drawing (package), 286305
igraph.BFSIter (class), 99
igraph.drawing.baseclasses (module), 306
igraph.BFSIter.__iter__ (method), 99
309
igraph.BFSIter.next (method), 99
igraph.drawing.colors (module), 310322
igraph.clustering (module), 232259
igraph.drawing.coord (module), 323325
igraph.clustering.Clustering (class), 236
igraph.drawing.edge (module), 326334
239
igraph.drawing.graph (module), 334340
igraph.clustering.CohesiveBlocks (class),
igraph.drawing.metamagic (module), 341
256259
344
igraph.clustering.compare_communities
igraph.drawing.Plot (class), 301305
(function), 234
igraph.drawing.plot (function), 288
igraph.clustering.Cover (class), 250253
igraph.drawing.shapes (module), 345347
igraph.clustering.Dendrogram (class), 245
igraph.drawing.text (module), 348352
248
igraph.drawing.utils (module), 353363
igraph.clustering.split_join_distance (funcigraph.drawing.vertex (module), 364368
tion), 234
igraph.Edge (class), 99103
igraph.clustering.VertexClustering (class),
igraph.Edge.__delitem__ (method), 100
239245
igraph.Edge.__eq__ (method), 100
igraph.clustering.VertexCover (class), 253
igraph.Edge.__ge__ (method), 100
256
igraph.Edge.__getitem__ (method), 100
igraph.clustering.VertexDendrogram (class), igraph.Edge.__gt__ (method), 100
248250
igraph.Edge.__le__ (method), 100
igraph.compat (module), 260
igraph.Edge.__len__ (method), 100

421

INDEX

igraph.Edge.lt (method), 100

igraph.Edge.__ne__ (method), 101
igraph.Edge.__setitem__ (method), 101
igraph.Edge.attribute_names (method),
101
igraph.Edge.attributes (method), 101
igraph.Edge.count_multiple (method),
101
igraph.Edge.delete (method), 101
igraph.Edge.is_loop (method), 101
igraph.Edge.is_multiple (method), 102
igraph.Edge.is_mutual (method), 102
igraph.Edge.update_attributes (method),
102
igraph.EdgeSeq (class), 9297
igraph.EdgeSeq.__call__ (method), 95
igraph.EdgeSeq.attributes (method), 94
igraph.EdgeSeq.count_multiple (method),
96
igraph.EdgeSeq.delete (method), 96
igraph.EdgeSeq.edge_betweenness (method),
96
igraph.EdgeSeq.is_loop (method), 96
igraph.EdgeSeq.is_multiple (method), 96
igraph.EdgeSeq.is_mutual (method), 96
igraph.EdgeSeq.subgraph (method), 97
igraph.Graph (class), 1184
igraph.Graph.__add__ (method), 67
igraph.Graph.__coerce__ (method), 68
igraph.Graph.__iadd__ (method), 67
igraph.Graph.__isub__ (method), 68
igraph.Graph.__mul__ (method), 68
igraph.Graph.__nonzero__ (method),
68
igraph.Graph.__plot__ (method), 69
igraph.Graph.__sub__ (method), 68
igraph.Graph.add_edge (method), 21
igraph.Graph.add_vertex (method), 21
igraph.Graph.adjacent (method), 22
igraph.Graph.alpha (method), 13, 165
igraph.Graph.as_directed (method), 22
igraph.Graph.as_undirected (method),
22
igraph.Graph.biconnected_components
422

(method), 25
igraph.Graph.Bipartite (class method),
61
igraph.Graph.clusters (method), 26
igraph.Graph.cohesion (method), 14, 16,
211
igraph.Graph.community_leading_eigenvector_naive
(method), 37
igraph.Graph.count_automorphisms_vf2
(method), 35
igraph.Graph.cut_vertices (method), 13,
125
igraph.Graph.degree_distribution (method),
26
igraph.Graph.DictList (class method), 58
igraph.Graph.edge_disjoint_paths (method),
15, 17, 154
igraph.Graph.evcent (method), 13, 154
igraph.Graph.Formula (class method),
60
igraph.Graph.Full_Bipartite (class method),
62
igraph.Graph.get_adjedgelist (method),
28
igraph.Graph.get_adjlist (method), 27
igraph.Graph.get_automorphisms_vf2
(method), 36
igraph.Graph.get_inclist (method), 28
igraph.Graph.GRG (class method), 64
igraph.Graph.Incidence (class method),
64
igraph.Graph.indegree (method), 23
igraph.Graph.is_named (method), 29
igraph.Graph.is_weighted (method), 29
igraph.Graph.k_core (method), 45
igraph.Graph.layout (method), 45
igraph.Graph.layout_auto (method), 46
igraph.Graph.layout_fruchterman_reingold_3d
(method), 71
igraph.Graph.layout_grid_3d (method),
71
igraph.Graph.layout_kamada_kawai_3d
(method), 71
igraph.Graph.layout_random_3d (method),

INDEX

71
122
igraph.Graph.layout_sphere (method),
igraph.GraphBase.__getitem__ (method),
72
122
igraph.Graph.layout_sugiyama (method),
igraph.GraphBase.__invert__ (method),
47
122
igraph.Graph.maximum_bipartite_matching igraph.GraphBase.__or__ (method), 123
igraph.GraphBase.__rand__ (method),
(method), 48
igraph.Graph.omega (method), 13, 131
123
igraph.Graph.outdegree (method), 23
igraph.GraphBase.__ror__ (method),
igraph.Graph.pagerank (method), 32
123
igraph.Graph.Random_Bipartite (class
igraph.GraphBase.__setitem__ (method),
123
method), 63
igraph.Graph.Read (class method), 54,
igraph.GraphBase.add_edges (method),
55
123
igraph.Graph.Read_Adjacency (class method), igraph.GraphBase.add_vertices (method),
49
123
igraph.Graph.Read_GraphMLz (class method),igraph.GraphBase.Adjacency (method),
51
104
igraph.Graph.Read_Pickle (class method),
igraph.GraphBase.all_minimal_st_separators
(method), 123
52
igraph.Graph.Read_Picklez (class method), igraph.GraphBase.all_st_cuts (method),
53
124
igraph.Graph.shell_index (method), 13,
igraph.GraphBase.all_st_mincuts (method),
145
124
igraph.Graph.shortest_paths_dijkstra (method),
igraph.GraphBase.are_connected (method),
18, 197
124
igraph.Graph.spanning_tree (method),
igraph.GraphBase.assortativity (method),
33
125
igraph.Graph.subgraph (method), 19, 166
igraph.GraphBase.assortativity_degree
igraph.Graph.summary (method), 71
(method), 126
igraph.Graph.TupleList (class method),
igraph.GraphBase.assortativity_nominal
59
(method), 127
igraph.Graph.write (method), 56, 57
igraph.GraphBase.Asymmetric_Preference
igraph.Graph.write_adjacency (method),
(method), 104
49
igraph.GraphBase.Atlas (method), 105
igraph.Graph.write_graphmlz (method),
igraph.GraphBase.attributes (method),
50
127
igraph.Graph.write_pickle (method), 52
igraph.GraphBase.authority_score (method),
igraph.Graph.write_picklez (method), 52
127
igraph.Graph.write_svg (method), 53
igraph.GraphBase.average_path_length
igraph.GraphBase (class), 103215
(method), 128
igraph.GraphBase.__and__ (method),
igraph.GraphBase.Barabasi (method), 105
122
igraph.GraphBase.betweenness (method),
igraph.GraphBase.__delitem__ (method),
128
423

INDEX

igraph.GraphBase.bfs (method), 129

igraph.GraphBase.convergence_degree (method),
igraph.GraphBase.bfsiter (method), 129
145
igraph.GraphBase.bibcoupling (method),
igraph.GraphBase.convergence_field_size
(method), 145
130
igraph.GraphBase.biconnected_components igraph.GraphBase.copy (method), 145
(method), 130
igraph.GraphBase.count_isomorphisms_vf2
igraph.GraphBase.bipartite_projection
(method), 146
(method), 130
igraph.GraphBase.count_multiple (method),
igraph.GraphBase.bipartite_projection_size
147
(method), 130
igraph.GraphBase.count_subisomorphisms_vf2
igraph.GraphBase.canonical_permutation
(method), 148
igraph.GraphBase.De_Bruijn (method),
(method), 130
igraph.GraphBase.cliques (method), 131
106
igraph.GraphBase.closeness (method), 132
igraph.GraphBase.decompose (method),
igraph.GraphBase.clusters (method), 133
149
igraph.GraphBase.cocitation (method),
igraph.GraphBase.degree (method), 150
134
igraph.GraphBase.Degree_Sequence (method),
igraph.GraphBase.cohesive_blocks (method),
107
134
igraph.GraphBase.delete_edges (method),
igraph.GraphBase.community_edge_betweenness
150
igraph.GraphBase.delete_vertices (method),
(method), 134
igraph.GraphBase.community_fastgreedy
150
(method), 135
igraph.GraphBase.density (method), 150
igraph.GraphBase.community_infomap
igraph.GraphBase.diameter (method), 151
(method), 136
igraph.GraphBase.difference (method),
igraph.GraphBase.community_label_propagation
151
(method), 137
igraph.GraphBase.disjoint_union (method),
igraph.GraphBase.community_leading_eigenvector
151
(method), 138
igraph.GraphBase.diversity (method), 151
igraph.GraphBase.community_multilevel
igraph.GraphBase.dyad_census (method),
(method), 139
152
igraph.GraphBase.community_optimal_modularity
igraph.GraphBase.eccentricity (method),
(method), 140
152
igraph.GraphBase.community_spinglass
igraph.GraphBase.ecount (method), 153
(method), 141
igraph.GraphBase.edge_attributes (method),
igraph.GraphBase.community_walktrap
153
(method), 142
igraph.GraphBase.edge_betweenness (method),
igraph.GraphBase.complementer (method),
153
143
igraph.GraphBase.Erdos_Renyi (method),
igraph.GraphBase.compose (method), 143
108
igraph.GraphBase.constraint (method),
igraph.GraphBase.Establishment (method),
143
109
igraph.GraphBase.contract_vertices (method), igraph.GraphBase.Famous (method), 109
144
igraph.GraphBase.farthest_points (method),
424

INDEX

155
igraph.GraphBase.is_connected (method),
igraph.GraphBase.feedback_arc_set (method), 167
155
igraph.GraphBase.is_dag (method), 167
igraph.GraphBase.Forest_Fire (method),
igraph.GraphBase.is_directed (method),
109
167
igraph.GraphBase.Full (method), 110
igraph.GraphBase.is_loop (method), 167
igraph.GraphBase.Full_Citation (method),
igraph.GraphBase.is_minimal_separator
110
(method), 168
igraph.GraphBase.get_adjacency (method), igraph.GraphBase.is_multiple (method),
156
168
igraph.GraphBase.get_all_shortest_paths
igraph.GraphBase.is_mutual (method),
168
(method), 156
igraph.GraphBase.get_diameter (method),
igraph.GraphBase.is_separator (method),
157
169
igraph.GraphBase.get_edgelist (method),
igraph.GraphBase.is_simple (method),
157
169
igraph.GraphBase.get_eid (method), 157
igraph.GraphBase.Isoclass (method), 111
igraph.GraphBase.get_eids (method), 158
igraph.GraphBase.isoclass (method), 169
igraph.GraphBase.get_incidence (method),
igraph.GraphBase.isomorphic (method),
158
170
igraph.GraphBase.get_isomorphisms_vf2
igraph.GraphBase.isomorphic_bliss (method),
(method), 159
170
igraph.GraphBase.get_shortest_paths (method),
igraph.GraphBase.isomorphic_vf2 (method),
160
171
igraph.GraphBase.get_subisomorphisms_lad igraph.GraphBase.K_Regular (method),
(method), 161
111
igraph.GraphBase.get_subisomorphisms_vf2 igraph.GraphBase.Kautz (method), 111
(method), 162
igraph.GraphBase.knn (method), 172
igraph.GraphBase.girth (method), 163
igraph.GraphBase.laplacian (method), 173
igraph.GraphBase.gomory_hu_tree (method), igraph.GraphBase.largest_cliques (method),
164
173
igraph.GraphBase.Growing_Random (method),igraph.GraphBase.largest_independent_vertex_sets
110
(method), 174
igraph.GraphBase.has_multiple (method),
igraph.GraphBase.Lattice (method), 112
164
igraph.GraphBase.layout_bipartite (method),
igraph.GraphBase.hub_score (method),
174
164
igraph.GraphBase.layout_circle (method),
igraph.GraphBase.incident (method), 165
174
igraph.GraphBase.independent_vertex_sets igraph.GraphBase.layout_drl (method),
(method), 165
175
igraph.GraphBase.intersection (method),
igraph.GraphBase.layout_fruchterman_reingold
166
(method), 176
igraph.GraphBase.is_bipartite (method),
igraph.GraphBase.layout_graphopt (method),
166
177
425

INDEX

igraph.GraphBase.layout_grid (method),
igraph.GraphBase.neighborhood_size (method),
178
193
igraph.GraphBase.layout_grid_fruchterman_reingold
igraph.GraphBase.neighbors (method),
(method), 179
193
igraph.GraphBase.layout_kamada_kawai
igraph.GraphBase.path_length_hist (method),
(method), 180
194
igraph.GraphBase.layout_lgl (method),
igraph.GraphBase.permute_vertices (method),
181
194
igraph.GraphBase.layout_mds (method),
igraph.GraphBase.personalized_pagerank
182
(method), 194
igraph.GraphBase.layout_random (method), igraph.GraphBase.predecessors (method),
183
195
igraph.GraphBase.layout_reingold_tilford
igraph.GraphBase.Preference (method),
112
(method), 183
igraph.GraphBase.layout_reingold_tilford_circular
igraph.GraphBase.radius (method), 196
(method), 184
igraph.GraphBase.Read_DIMACS (method),
igraph.GraphBase.layout_star (method),
113
185
igraph.GraphBase.Read_DL (method),
igraph.GraphBase.LCF (method), 112
113
igraph.GraphBase.linegraph (method), 185
igraph.GraphBase.Read_Edgelist (method),
igraph.GraphBase.maxdegree (method),
114
185
igraph.GraphBase.Read_GML (method),
igraph.GraphBase.maxflow (method), 186
114
igraph.GraphBase.maxflow_value (method), igraph.GraphBase.Read_GraphDB (method),
186
114
igraph.GraphBase.maximal_cliques (method), igraph.GraphBase.Read_GraphML (method),
187
114
igraph.GraphBase.maximal_independent_vertex_sets
igraph.GraphBase.Read_Lgl (method),
(method), 187
114
igraph.GraphBase.mincut (method), 187
igraph.GraphBase.Read_Ncol (method),
igraph.GraphBase.mincut_value (method),
115
188
igraph.GraphBase.Read_Pajek (method),
igraph.GraphBase.minimum_size_separators 116
igraph.GraphBase.Recent_Degree (method),
(method), 189
igraph.GraphBase.modularity (method),
116
189
igraph.GraphBase.reciprocity (method),
igraph.GraphBase.motifs_randesu (method),
196
190
igraph.GraphBase.rewire (method), 196
igraph.GraphBase.motifs_randesu_estimate igraph.GraphBase.rewire_edges (method),
(method), 191
197
igraph.GraphBase.motifs_randesu_no (method),
igraph.GraphBase.Ring (method), 117
192
igraph.GraphBase.SBM (method), 117
igraph.GraphBase.neighborhood (method),
igraph.GraphBase.similarity_dice (method),
192
198
426

INDEX

igraph.GraphBase.similarity_inverse_log_weighted
igraph.GraphBase.Watts_Strogatz (method),
(method), 199
121
igraph.GraphBase.similarity_jaccard (method),igraph.GraphBase.Weighted_Adjacency
(method), 121
200
igraph.GraphBase.simplify (method), 201
igraph.GraphBase.write_dimacs (method),
igraph.GraphBase.st_mincut (method),
212
202
igraph.GraphBase.write_dot (method),
igraph.GraphBase.Star (method), 118
213
igraph.GraphBase.Static_Fitness (method), igraph.GraphBase.write_edgelist (method),
118
213
igraph.GraphBase.Static_Power_Law (method),
igraph.GraphBase.write_gml (method),
119
213
igraph.GraphBase.strength (method), 203
igraph.GraphBase.write_graphml (method),
igraph.GraphBase.subcomponent (method),
213
203
igraph.GraphBase.write_leda (method),
igraph.GraphBase.subgraph_edges (method),
214
204
igraph.GraphBase.write_lgl (method), 214
igraph.GraphBase.subisomorphic_lad (method),igraph.GraphBase.write_ncol (method),
204
214
igraph.GraphBase.subisomorphic_vf2 (method),igraph.GraphBase.write_pajek (method),
205
215
igraph.GraphBase.successors (method),
igraph.layout (module), 369375
206
igraph.layout.Layout (class), 369375
igraph.GraphBase.to_directed (method),
igraph.matching (module), 376379
207
igraph.matching.Matching (class), 376
igraph.GraphBase.to_undirected (method),
379
207
igraph.read (function), 4
igraph.GraphBase.topological_sorting (method),
igraph.remote (package), 380
207
igraph.remote.gephi (module), 381387
igraph.GraphBase.transitivity_avglocal_undirected
igraph.remote.nexus (module), 388392
(method), 207
igraph.statistics (module), 393403
igraph.GraphBase.transitivity_local_undirected
igraph.statistics.FittedPowerLaw (class),
(method), 208
396398
igraph.GraphBase.transitivity_undirected
igraph.statistics.Histogram (class), 398
(method), 209
400
igraph.GraphBase.Tree (method), 120
igraph.statistics.mean (function), 393
igraph.GraphBase.triad_census (method),
igraph.statistics.median (function), 393
210
igraph.statistics.percentile (function), 394
igraph.GraphBase.unfold_tree (method),
igraph.statistics.power_law_fit (function),
210
394
igraph.GraphBase.union (method), 211
igraph.statistics.quantile (function), 395
igraph.GraphBase.vcount (method), 211
igraph.statistics.RunningMean (class),
igraph.GraphBase.vertex_attributes (method), 400403
211
igraph.summary (function), 5
427

INDEX

igraph.summary (module), 404406

10
igraph.summary.GraphSummary (class),
igraph.Vertex.predecessors (method), 10
404406
igraph.Vertex.shortest_paths (method),
igraph.utils (module), 407414
10
igraph.utils.multidict (class), 409414
igraph.Vertex.strength (method), 10
igraph.utils.named_temporary_file (funcigraph.Vertex.successors (method), 10
igraph.Vertex.update_attributes (method),
tion), 407
igraph.utils.rescale (function), 407
11
igraph.utils.safemax (function), 408
igraph.VertexSeq (class), 8492
igraph.utils.safemin (function), 409
igraph.VertexSeq.__call__ (method),
igraph.Vertex (class), 611
87
igraph.Vertex.__delitem__ (method),
igraph.VertexSeq.attributes (method), 86
6
igraph.VertexSeq.betweenness (method),
igraph.Vertex.__eq__ (method), 6
88
igraph.Vertex.__ge__ (method), 6
igraph.VertexSeq.bibcoupling (method),
igraph.Vertex.__getitem__ (method),
88
6
igraph.VertexSeq.closeness (method), 88
igraph.Vertex.__gt__ (method), 6
igraph.VertexSeq.cocitation (method), 88
igraph.Vertex.__le__ (method), 7
igraph.VertexSeq.constraint (method), 88
igraph.Vertex.__len__ (method), 7
igraph.VertexSeq.degree (method), 88
igraph.Vertex.__lt__ (method), 7
igraph.VertexSeq.delete (method), 89
igraph.Vertex.__ne__ (method), 7
igraph.VertexSeq.diversity (method), 89
igraph.Vertex.__setitem__ (method),
igraph.VertexSeq.eccentricity (method),
7
89
igraph.Vertex.attribute_names (method),
igraph.VertexSeq.get_shortest_paths (method),
7
89
igraph.Vertex.attributes (method), 7
igraph.VertexSeq.indegree (method), 89
igraph.Vertex.betweenness (method), 7
igraph.VertexSeq.is_minimal_separator
igraph.Vertex.closeness (method), 8
(method), 90
igraph.Vertex.constraint (method), 8
igraph.VertexSeq.is_separator (method),
igraph.Vertex.degree (method), 8
90
igraph.Vertex.delete (method), 8
igraph.VertexSeq.isoclass (method), 90
igraph.Vertex.diversity (method), 8
igraph.VertexSeq.maxdegree (method),
igraph.Vertex.eccentricity (method), 8
90
igraph.Vertex.get_shortest_paths (method), igraph.VertexSeq.outdegree (method), 90
9
igraph.VertexSeq.pagerank (method), 91
igraph.Vertex.indegree (method), 9
igraph.VertexSeq.personalized_pagerank
igraph.Vertex.is_minimal_separator (method), (method), 91
9
igraph.VertexSeq.shortest_paths (method),
igraph.Vertex.is_separator (method), 9
91
igraph.Vertex.neighbors (method), 9
igraph.VertexSeq.similarity_dice (method),
igraph.Vertex.outdegree (method), 9
91
igraph.Vertex.pagerank (method), 10
igraph.VertexSeq.similarity_jaccard (method),
igraph.Vertex.personalized_pagerank (method), 91
428

INDEX

igraph.VertexSeq.subgraph (method), 92
igraph.write (function), 4

429

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Python Igraph

Uploaded by

Python Igraph

Uploaded by

igraph library

10.7 Class Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301

25.2 Class NexusConnection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 388

_igraph: Low-level Python interface for the igraph library.

(Section 16, p. 341)

the graph on which the calculation will be run

the graph to be saved

filename: the name of the file to be written

save(graph, filename, *args, **kwds)

the graph to be saved

filename: the name of the file to be written

Inherited from object

evcent(directed =True, scale=True, weights=None, return_eigenvalue=False,

whether to consider edge directions in a

whether to normalize the centralities so the

edge weights given as a list or an edge

return_eigenvalue: whether to return the actual largest

an ARPACKOptions object that can be used to

vertex_disjoint_paths(source=-1, target=-1, checks=True,

the source vertex involved in the calculation.

the target vertex involved in the calculation.

if the whole graph connectivity is calculated and this is

neighbors: tells igraph what to do when the two vertices are

edge_disjoint_paths(source=-1, target=-1, checks=True)

cohesion(source=-1, target=-1, checks=True, neighbors="error")

the source vertex involved in the calculation.

the target vertex involved in the calculation.

if the whole graph connectivity is calculated and this is

neighbors: tells igraph what to do when the two vertices are

adhesion(source=-1, target=-1, checks=True)

shortest_paths_dijkstra(source=None, target=None, weights=None,

the type of shortest paths to be used for the calculation in

a list containing the vertex IDs which should be

implementation: the implementation to use when constructing the

__init__(n=None, edges=None, directed =None, graph_attrs=None,

the number of vertices. Can be omitted, the default

the edge list where every list item is a pair of

whether the graph should be directed

graph_attrs: the attributes of the graph as a dictionary.

the attributes of the edges as a dictionary. Every

delete_edges(self, *args, **kwds)

None - deletes all edges

all_st_cuts(self, source, target)

the source vertex ID

the target vertex ID

capacity: the edge capacities (weights). If None, all edges have

either GET_ADJACENCY_LOWER (uses the lower triangle of

attribute: if None, returns the ordinary adjacency matrix. When

the default value written to the cells in the case of

specifies whether the edge IDs should be returned in the

gomory_hu_tree(capacity=None, flow ="flow")

the name of the edge attribute in the returned graph in

maxflow(source, target, capacity=None)

mincut(source=None, target=None, capacity=None)

the source vertex ID. If None, the target must also be

capacity: the edge capacities (weights). If None, all edges have

the source vertex ID

the target vertex ID

capacity: the capacity of the edges. It must be a list or a valid

optional edge weights or None if all edges are weighed

pagerank(self, vertices=None, directed =True, damping=0.85, weights=None,

the indices of the vertices being queried. None

whether to consider directed paths.

the damping factor. 1-damping is the PageRank

edge weights to be used. Can be a sequence or

arpack_options: an ARPACKOptions object used to fine-tune the

The number of iterations to use in the power

The power method implementation will consider

spanning_tree(self, weights=None, return_tree=True)

a vector containing weights for every edge in the

return_tree: whether to return the minimum spanning tree (when

transitivity_avglocal_undirected(self, mode=nan, weights=None)

defines how to treat vertices with degree less than two. If

weights: edge weights to be used. Can be a sequence or iterable or

count_automorphisms_vf2(self, color =None, edge_color =None,

community_infomap(self, edge_weights=None, vertex_weights=None,

init(n=None, edges=None, directed =None, graph_attrs=None,