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.
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attach
()¶ Attach this edge to the edge collections of the vertices.
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data
: object¶
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detach
()¶ Removes this edge from the edge collections of the vertices.
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feedback
: bool¶
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w
: int¶
graphistry.layout.graph.edgeBase module¶
graphistry.layout.graph.graph module¶
-
class
graphistry.layout.graph.graph.
Graph
(vertices=None, edges=None, directed=True)¶ Bases:
object
The graph is stored in disjoint-sets holding each connected component in components as a list of graph_core objects.
- Attributes
C (list[GraphBase]): list of graph_core components.
- Methods
add_vertex(v): add vertex v into the Graph as a new component add_edge(e): add edge e and its vertices into the Graph possibly merging the associated graph_core components get_vertices_count(): see order() vertices(): see graph_core edges(): see graph_core remove_edge(e): remove edge e possibly spawning two new cores if the graph_core that contained e gets disconnected. remove_vertex(v): remove vertex v and all its edges. order(): the order of the graph (number of vertices) norm(): the norm of the graph (number of edges) deg_min(): the minimum degree of vertices deg_max(): the maximum degree of vertices deg_avg(): the average degree of vertices eps(): the graph epsilon value (norm/order), average number of edges per vertex. connected(): returns True if the graph is connected (i.e. it has only one component). components(): returns the list of components
-
N
(v, f_io=0)¶
-
add_edge
(e)¶
-
add_edges
(edges)¶ - Parameters
edges (
List
) –
-
add_vertex
(v)¶
-
component_class
¶
-
connected
()¶
-
deg_avg
()¶
-
deg_max
()¶
-
deg_min
()¶
-
edges
()¶
-
eps
()¶
-
get_vertex_from_data
(data)¶
-
get_vertices_count
()¶
-
norm
()¶
-
order
()¶
-
path
(x, y, f_io=0, hook=None)¶
-
remove_edge
(e)¶
-
remove_vertex
(x)¶
-
vertices
()¶
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.
- Methods:
vertices(cond=None): generates an iterator over vertices, with optional filter edges(cond=None): generates an iterator over edges, with optional filter matrix(cond=None): returns the associativity matrix of the graph component order(): the order of the graph (number of vertices) norm(): the norm of the graph (number of edges) deg_min(): the minimum degree of vertices deg_max(): the maximum degree of vertices deg_avg(): the average degree of vertices eps(): the graph epsilon value (norm/order), average number of edges per vertex. 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. roots(): returns the list of roots (vertices with no inward edges). leaves(): returns the list of leaves (vertices with no outward edges). add_single_vertex(v): allow a GraphBase to hold a single vertex. add_edge(e): add edge e. At least one of its vertex must belong to the graph, the other being added automatically. remove_edge(e): remove Edge e, asserting that the resulting graph is still connex. remove_vertex(x): remove Vertex x and all associated edges. 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. get_scs_with_feedback(): 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). partition(): returns a partition of the connected graph as a list of lists. neighbors(v): returns neighbours of a vertex v.
-
N
(v, f_io=0)¶
-
add_edge
(e)¶
-
add_single_vertex
(v)¶
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complement
(G)¶
-
constant_function
(value)¶
-
contract
(e)¶
-
deg_avg
()¶
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deg_max
()¶
-
deg_min
()¶
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dft
(start_vertex=None)¶
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dijkstra
(x, f_io=0, hook=None)¶
-
edges
(cond=None)¶
-
eps
()¶
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get_scs_with_feedback
(roots=None)¶ Minimum FAS algorithm (feedback arc set) creating a DAG.
- Parameters
roots –
- Returns
-
leaves
()¶
-
matrix
(cond=None)¶ This associativity matrix is like the adjacency matrix but antisymmetric.
- Parameters
cond – same a the condition function in vertices().
- Returns
array
-
norm
()¶ The size of the edge poset.
-
order
()¶
-
partition
()¶
-
path
(x, y, f_io=0, hook=None)¶
-
remove_edge
(e)¶
-
remove_vertex
(x)¶
-
roots
()¶
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spans
(vertices)¶
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union_update
(G)¶
-
vertices
(cond=None)¶
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.
- Methods
degree() : degree of the vertex (number of edges). e_in() : list of edges directed toward this vertex. e_out(): list of edges directed outward this vertex. e_dir(int): either e_in, e_out or all edges depending on provided direction parameter (>0 means outward). neighbors(f_io=0): list of neighbor vertices in all directions (default) or in filtered f_io direction (>0 means outward). e_to(v): returns the Edge from this vertex directed toward vertex v. e_from(v): returns the Edge from vertex v directed toward this vertex. e_with(v): return the Edge with both this vertex and vertex v detach(): removes this vertex from all its edges and returns this list of edges.
-
degree
()¶
-
detach
()¶
-
e_dir
(dir)¶
-
e_from
(x)¶
-
e_in
()¶
-
e_out
()¶
-
e_to
(y)¶
-
e_with
(v)¶
-
neighbors
(direction=0)¶ Returns the neighbors of this vertex.
- Parameters
direction –
0: parent and children
-1: parents
+1: children
- Returns
list of vertices