Source code for indra.assemblers.pysb.kappa_util

from __future__ import absolute_import, print_function, unicode_literals
from builtins import dict, str
from networkx import MultiDiGraph
from pygraphviz import AGraph


[docs]def im_json_to_graph(im_json): """Return networkx graph from Kappy's influence map JSON. Parameters ---------- im_json : dict A JSON dict which contains an influence map generated by Kappy. Returns ------- graph : networkx.MultiDiGraph A graph representing the influence map. """ imap_data = im_json['influence map']['map'] # Initialize the graph graph = MultiDiGraph() id_node_dict = {} # Add each node to the graph for node_dict in imap_data['nodes']: # There is always just one entry here with the node type e.g. "rule" # as key, and all the node data as the value node_type, node = list(node_dict.items())[0] # Add the node to the graph with its label and type attrs = {'fillcolor': '#b7d2ff' if node_type == 'rule' else '#cdffc9', 'shape': 'box' if node_type == 'rule' else 'oval', 'style': 'filled'} graph.add_node(node['label'], node_type=node_type, **attrs) # Save the key of the node to refer to it later new_key = '%s%s' % (node_type, node['id']) id_node_dict[new_key] = node['label'] def add_edges(link_list, edge_sign): attrs = {'sign': edge_sign, 'color': 'green' if edge_sign == 1 else 'red', 'arrowhead': 'normal' if edge_sign == 1 else 'tee'} for link_dict in link_list: source = link_dict['source'] for target_dict in link_dict['target map']: target = target_dict['target'] src_id = '%s%s' % list(source.items())[0] tgt_id = '%s%s' % list(target.items())[0] graph.add_edge(id_node_dict[src_id], id_node_dict[tgt_id], **attrs) # Add all the edges from the positive and negative influences add_edges(imap_data['wake-up map'], 1) add_edges(imap_data['inhibition map'], -1) return graph
[docs]def cm_json_to_graph(im_json): """Return pygraphviz Agraph from Kappy's contact map JSON. Parameters ---------- im_json : dict A JSON dict which contains a contact map generated by Kappy. Returns ------- graph : pygraphviz.Agraph A graph representing the contact map. """ cmap_data = im_json['contact map']['map'] # Initialize the graph graph = AGraph() # In this loop we add sites as nodes and clusters around sites to the # graph. We also collect edges to be added between sites later. edges = [] for node_idx, node in enumerate(cmap_data): sites_in_node = [] for site_idx, site in enumerate(node['node_sites']): # We map the unique ID of the site to its name site_key = (node_idx, site_idx) sites_in_node.append(site_key) graph.add_node(site_key, label=site['site_name'], style='filled', shape='ellipse') # Each port link is an edge from the current site to the # specified site if not site['site_type'] or not site['site_type'][0] == 'port': continue for port_link in site['site_type'][1]['port_links']: edge = (site_key, tuple(port_link)) edges.append(edge) graph.add_subgraph(sites_in_node, name='cluster_%s' % node['node_type'], label=node['node_type']) # Finally we add the edges between the sites for source, target in edges: graph.add_edge(source, target) return graph