Causal analysis graphs (indra.assemblers.cag_assembler)

class indra.assemblers.cag_assembler.CAGAssembler(stmts=None, grounding_threshold=None)[source]

Assembles a causal analysis graph from INDRA Statements.

Parameters:stmts (Optional[list[indra.statement.Statements]]) – A list of INDRA Statements to be assembled. Currently supports Influence Statements.
statements

list[indra.statements.Statement] – A list of INDRA Statements to be assembled.

CAG

nx.MultiDiGraph – A networkx MultiDiGraph object representing the causal analysis graph.

add_statements(stmts)[source]

Add a list of Statements to the assembler.

export_to_cytoscapejs()[source]

Return CAG in format readable by CytoscapeJS.

Returns:A JSON-like dict representing the graph for use with CytoscapeJS.
Return type:dict
make_model(grounding_threshold=None)[source]

Return a networkx MultiDiGraph representing a causal analysis graph.

Parameters:grounding_threshold (Optional[float]) – Minimum threshold score for Eidos grounding.
Returns:The assembled CAG.
Return type:nx.MultiDiGraph