Graph

Module provides basic Graph classes.

class AnnotatedGraph(name=None, n_vertices=None, edges=None, directed=False, vertex_coordinates=None, vertex_radii=None, edge_coordinates=None, edge_radii=None, edge_geometries=None, shape=None, vertex_labels=None, edge_labels=None, annotation=None)

Bases: ClearMap.Analysis.Graphs.Graph.GeometricGraph

Base class for graphs whose vertices are embedded in an Eucledian space and have an annotation.

edge_annotation()

set_edge_annotation(value)

set_vertex_annotation(value)

vertex_annotation()

property annotation

class GeometricGraph(name=None, n_vertices=None, edges=None, directed=False, vertex_coordinates=None, vertex_radii=None, edge_coordinates=None, edge_radii=None, edge_geometries=None, shape=None)

Bases: ClearMap.Analysis.Graphs.Graph.Graph

Base class for graphs whose vertices are embedded in an Eucledian space.

edge_coordinates(edge=None)

edge_coordinates_from_vertex_coordinates()

edge_geometry(*args, **kwargs)

edge_radii(edge=None)

edge_radii_from_vertex_radii()

edge_vectors(normalize=False)

expand_edge_geometry()

reduce_edge_geometry()

set_edge_coordinates(coordinates, axis=None, edge=None)

set_edge_geometry(*args, **kwargs)

set_edge_radii(edge=None)

set_vertex_coordinates(coordinates, axis=None, vertex=None)

set_vertex_radii(radius, vertex=None)

vertex_coordinates(axis=None, vertex=None)

vertex_radii(vertex=None)

property edge_geometry_type

property has_edge_geometry

property ndim

property shape

The shape of the underlying space in which the graph is embedded.

class Graph(name=None, n_vertices=None, edges=None, directed=None)

Bases: object

Abstract base Graph class.

All graph interfaces should inherit from the class.

add_edge(edge)

add_edge_property(name, source, dtype=None)

add_vertex(n_vertices=None, index=None, vertex=None)

add_vertex_property(name, source, dtype=None)

edge(edge)

edge_connectivity()

edge_properties()

edge_property(name)

load(filename)

remove_edge(edge)

remove_edge_property(name)

remove_vertex(index=None, vertex=None)

remove_vertex_property(name)

save(filename)

set_edge_property(name, source)

set_vertex_property(name, source)

vertex(index)

vertex_degree(index)

vertex_degrees()

vertex_in_degree(index)

vertex_in_degrees()

vertex_out_degree(index)

vertex_out_degrees()

vertex_properties()

vertex_property(name, index=None)

property directed

property edges

property n_edges

Number of edges in the graph.

property n_vertices

Number of vertices in the graph.

property name

property vertices

load(filename)

save(filename, graph)