Causal analysis graphs (`indra.assemblers.cag.assembler`)¶

class indra.assemblers.cag.assembler.CAGAssembler(stmts=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¶

A list of INDRA Statements to be assembled.

Type:	list[indra.statements.Statement]

CAG¶

A networkx MultiDiGraph object representing the causal analysis graph.

Type:	nx.MultiDiGraph

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

generate_jupyter_js(cyjs_style=None, cyjs_layout=None)[source]¶

Generate Javascript from a template to run in Jupyter notebooks.

Parameters:	cyjs_style (Optional[dict]) – A dict that sets CytoscapeJS style as specified in https://github.com/cytoscape/cytoscape.js/blob/master/documentation/md/style.md. cyjs_layout (Optional[dict]) – A dict that sets CytoscapeJS layout parameters.
Returns:	A Javascript string to be rendered in a Jupyter notebook cell.
Return type:	str

make_model(grounding_ontology='UN', grounding_threshold=None)[source]¶

Return a networkx MultiDiGraph representing a causal analysis graph.

Parameters:	grounding_ontology (Optional[str]) – The ontology from which the grounding should be taken (e.g. UN, FAO) grounding_threshold (Optional[float]) – Minimum threshold score for Eidos grounding.
Returns:	The assembled CAG.
Return type:	nx.MultiDiGraph

Causal analysis graphs (indra.assemblers.cag.assembler)¶