Cytoscape JS networks (indra.assemblers.cyjs.assembler)

class indra.assemblers.cyjs.assembler.CyJSAssembler(stmts=None)

This class assembles a CytoscapeJS graph from a set of INDRA Statements.

CytoscapeJS is a web-based network library for analysis and visualisation: http://js.cytoscape.org/

Parameters

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

statements

A list of INDRA Statements to be assembled.

Type

list[indra.statements.Statement]

add_statements(stmts)

Add INDRA Statements to the assembler’s list of statements.

Parameters

stmts (list[indra.statements.Statement]) – A list of indra.statements.Statement to be added to the statement list of the assembler.

get_gene_names()

Gather gene names of all nodes and node members

make_model(*args, **kwargs)

Assemble a Cytoscape JS network from INDRA Statements.

This method assembles a Cytoscape JS network from the set of INDRA Statements added to the assembler.

Parameters

grouping (bool) – If True, the nodes with identical incoming and outgoing edges are grouped and the corresponding edges are merged.

Returns

cyjs_str – The json serialized Cytoscape JS model.

Return type

str

print_cyjs_context()

Return a list of node names and their respective context.

Returns

cyjs_str_context – A json string of the context dictionary. e.g. - {‘CCLE’ : {‘bin_expression’ : {‘cell_line1’ : {‘gene1’:’val1’} }, ‘bin_expression’ : {‘cell_line’ : {‘gene1’:’val1’} } }}

Return type

str

print_cyjs_graph()

Return the assembled Cytoscape JS network as a json string.

Returns

cyjs_str – A json string representation of the Cytoscape JS network.

Return type

str

save_json(fname_prefix='model')

Save the assembled Cytoscape JS network in a json file.

This method saves two files based on the file name prefix given. It saves one json file with the graph itself, and another json file with the context.

Parameters

fname_prefix (Optional[str]) – The prefix of the files to save the Cytoscape JS network and context to. Default: model

save_model(fname='model.js')

Save the assembled Cytoscape JS network in a js file.

Parameters

file_name (Optional[str]) – The name of the file to save the Cytoscape JS network to. Default: model.js

set_CCLE_context(cell_types)

Set context of all nodes and node members from CCLE.