vivarium.library.make_network module

Make formatted files for Gephi Network Visualization

@organization: Covert Lab, Department of Bioengineering, Stanford University

vivarium.library.make_network.collapse_network(nodes, edges, remove_nodes_list)

remove_nodes (list) – nodes to be removed

vivarium.library.make_network.get_loose_nodes(stoichiometry)

vivarium.library.make_network.get_reactions(stoichiometry, molecules)

for each entry in molecules (list), return all the reactions with the molecules coefficient

vivarium.library.make_network.make_network(stoichiometry, info={})

Makes a gephi network info can contain node_sizes, node_types info = {

‘node_sizes’: node_sizes (dict), ‘node_types’: node_types (dict)

}

vivarium.library.make_network.save_network(nodes, edges, plotOutDir='out/network')

Save nodes and edges

Requires:

• nodes (dict) with {node_id: {‘label’ (str), ‘type’ (str), size (float)}}

• edges (list) with [[node_id1, node_id2] …]