Node-edge graphs (indra.assemblers.graph.assembler)

class indra.assemblers.graph.assembler.GraphAssembler(stmts=None, graph_properties=None, node_properties=None, edge_properties=None)[source]

The Graph assembler assembles INDRA Statements into a Graphviz node-edge graph.

Parameters

  • stmts (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to be added to the assembler’s list of Statements.

  • graph_properties (Optional[dict[str: str]]) – A dictionary of graphviz graph properties overriding the default ones.

  • node_properties (Optional[dict[str: str]]) – A dictionary of graphviz node properties overriding the default ones.

  • edge_properties (Optional[dict[str: str]]) – A dictionary of graphviz edge properties overriding the default ones.

statements

A list of INDRA Statements to be assembled.

Type

list[indra.statements.Statement]

graph

A pygraphviz graph that is assembled by this assembler.

Type

pygraphviz.AGraph

existing_nodes

The list of nodes (identified by node key tuples) that are already in the graph.

Type

list[tuple]

existing_edges

The list of edges (identified by edge key tuples) that are already in the graph.

Type

list[tuple]

graph_properties

A dictionary of graphviz graph properties used for assembly.

Type

dict[str: str]

node_properties

A dictionary of graphviz node properties used for assembly.

Type

dict[str: str]

edge_properties

A dictionary of graphviz edge properties used for assembly. Note that most edge properties are determined based on the type of the edge by the assembler (e.g. color, arrowhead). These settings cannot be directly controlled through the API.

Type

dict[str: str]

add_statements(stmts)[source]

Add a list of statements to be assembled.

Parameters

stmts (list[indra.statements.Statement]) – A list of INDRA Statements to be appended to the assembler’s list.

get_string()[source]

Return the assembled graph as a string.

Returns

graph_string – The assembled graph as a string.

Return type

str

make_model()[source]

Assemble the graph from the assembler’s list of INDRA Statements.

save_dot(file_name='graph.dot')[source]

Save the graph in a graphviz dot file.

Parameters

file_name (Optional[str]) – The name of the file to save the graph dot string to.

save_pdf(file_name='graph.pdf', prog='dot')[source]

Draw the graph and save as an image or pdf file.

Parameters

  • file_name (Optional[str]) – The name of the file to save the graph as. Default: graph.pdf

  • prog (Optional[str]) – The graphviz program to use for graph layout. Default: dot