graphistry.layout.graph package

Submodules

graphistry.layout.graph.edge module

class graphistry.layout.graph.edge.Edge(x, y, w=1, data=None, connect=False)

Bases: graphistry.layout.graph.edgeBase.EdgeBase

A graph edge.

Attributes

• data (object): an optional payload

• w (int): an optional weight associated with the edge (default 1) used by Dijkstra to find min-flow paths.

• feedback (bool): whether the Tarjan algorithm has inverted this edge to de-cycle the graph.

attach()

Attach this edge to the edge collections of the vertices.

data: object

degree: int

Is 0 if a loop, otherwise 1.

detach()

Removes this edge from the edge collections of the vertices.

feedback: bool

w: int

graphistry.layout.graph.edgeBase module

class graphistry.layout.graph.edgeBase.EdgeBase(x, y)

Bases: object

Base class for edges.

Attributes

• degree (int): degree of the edge (number of unique vertices).

• v (list[Vertex]): list of vertices associated with this edge.

degree: int

Is 0 if a loop, otherwise 1.

graphistry.layout.graph.graph module

class graphistry.layout.graph.graph.Graph(vertices=None, edges=None, directed=True)

Bases: object

N(v, f_io=0)

add_edge(e)

add edge e and its vertices into the Graph possibly merging the associated graph_core components

add_edges(edges)

Parameters

edges (List) –

add_vertex(v)

add vertex v into the Graph as a new component

component_class

alias of graphistry.layout.graph.graphBase.GraphBase

connected()

returns the list of components

deg_avg()

the average degree of vertices

deg_max()

the maximum degree of vertices

deg_min()

the minimum degree of vertices

edges()

eps()

the graph epsilon value (norm/order), average number of edges per vertex.

get_vertex_from_data(data)

get_vertices_count()

norm()

the norm of the graph (number of edges)

order()

the order of the graph (number of vertices)

path(x, y, f_io=0, hook=None)

remove_edge(e)

remove edge e possibly spawning two new cores if the graph_core that contained e gets disconnected.

remove_vertex(x)

remove vertex v and all its edges.

vertices()

see graph_core

graphistry.layout.graph.graphBase module

class graphistry.layout.graph.graphBase.GraphBase(vertices=None, edges=None, directed=True)

Bases: object

A connected graph of Vertex/Edge objects. A GraphBase is a component of a Graph that contains a connected set of Vertex and Edges.

Attributes:

verticesPoset (Poset[Vertex]): the partially ordered set of vertices of the graph. edgesPoset (Poset[Edge]): the partially ordered set of edges of the graph. loops (set[Edge]): the set of loop edges (of degree 0). directed (bool): indicates if the graph is considered oriented or not.

N(v, f_io=0)

add_edge(e)

add edge e. At least one of its vertex must belong to the graph, the other being added automatically.

add_single_vertex(v)

allow a GraphBase to hold a single vertex.

complement(G)

constant_function(value)

contract(e)

deg_avg()

the average degree of vertices

deg_max()

the maximum degree of vertices

deg_min()

the minimum degree of vertices

dft(start_vertex=None)

dijkstra(x, f_io=0, hook=None)

shortest weighted-edges paths between x and all other vertices by dijkstra’s algorithm with heap used as priority queue.

edges(cond=None)

generates an iterator over edges, with optional filter

eps()

the graph epsilon value (norm/order), average number of edges per vertex.

get_scs_with_feedback(roots=None)

Minimum FAS algorithm (feedback arc set) creating a DAG. Returns the set of strongly connected components (“scs”) by using Tarjan algorithm. These are maximal sets of vertices such that there is a path from each vertex to every other vertex. The algorithm performs a DFS from the provided list of root vertices. A cycle is of course a strongly connected component,but a strongly connected component can include several cycles. The Feedback Acyclic Set of edge to be removed/reversed is provided by marking the edges with a “feedback” flag. Complexity is O(V+E).

Parameters

roots –

Returns

leaves()

returns the list of leaves (vertices with no outward edges).

matrix(cond=None)

This associativity matrix is like the adjacency matrix but antisymmetric. Returns the associativity matrix of the graph component

Parameters

cond – same a the condition function in vertices().

Returns

array

norm()

The size of the edge poset (number of edges).

order()

the order of the graph (number of vertices)

partition()

path(x, y, f_io=0, hook=None)

shortest path between vertices x and y by breadth-first descent, contrained by f_io direction if provided. The path is returned as a list of Vertex objects. If a hook function is provided, it is called at every vertex added to the path, passing the vertex object as argument.

remove_edge(e)

remove Edge e, asserting that the resulting graph is still connex.

remove_vertex(x)

remove Vertex x and all associated edges.

roots()

returns the list of roots (vertices with no inward edges).

spans(vertices)

union_update(G)

vertices(cond=None)

generates an iterator over vertices, with optional filter

graphistry.layout.graph.vertex module

class graphistry.layout.graph.vertex.Vertex(data=None)

Bases: graphistry.layout.graph.vertexBase.VertexBase

Vertex class enhancing a VertexBase with graph-related features.

Attributes

component (GraphBase): the component of connected vertices that contains this vertex. By default, a vertex belongs no component but when it is added in a graph, c points to the connected component in this graph. data (object) : an object associated with the vertex.

property index

graphistry.layout.graph.vertexBase module

class graphistry.layout.graph.vertexBase.VertexBase

Bases: object

Base class for vertices.

Attributes

e (list[Edge]): list of edges associated with this vertex.

degree()

degree() : degree of the vertex (number of edges).

detach()

removes this vertex from all its edges and returns this list of edges.

e_dir(dir)

either e_in, e_out or all edges depending on provided direction parameter (>0 means outward).

e_from(x)

returns the Edge from vertex v directed toward this vertex.

e_in()

e_in() : list of edges directed toward this vertex.

e_out()

e_out(): list of edges directed outward this vertex.

e_to(y)

returns the Edge from this vertex directed toward vertex v.

e_with(v)

return the Edge with both this vertex and vertex v

neighbors(direction=0)

Returns the neighbors of this vertex. List of neighbor vertices in all directions (default) or in filtered f_io direction (>0 means outward).

Parameters

direction –

• 0: parent and children

• -1: parents

• +1: children

Returns

list of vertices

Module contents

graphistry.layout.gib