build_graph: update doc

command_line/cadbiom_cmd/interaction_graph.py

@@ -36,6 +36,7 @@ import os
 import glob
 import itertools as it
 from collections import defaultdict, Counter
+import networkx as nx
 
 # Library imports
 import cadbiom.commons as cm
@@ -351,17 +352,53 @@ def build_graph(all_genes, all_stimuli, unique_genes_interactions,
                 unique_stimulis_interactions,
                 unique_genes_stimuli_interactions,
                 unique_molecule_stimuli_interactions):
-    """
+    """Make an interaction weighted graph based on the searched molecule of interest
+
+    :Edges:
+
+        * gene - gene: Two genes present simultaneously in a solution
+        * stimulus - stimulus: Two stimuli present simultaneously in a solution
+        * gene - stimulus: One gene and one stimulus present simultaneously in
+          a solution (deprecated)
+        * molecule of interest - stimulus: A molecule of interest in a trajectory
+          related to a solution that contains a stimulus.
+
+    :Legend of the edges:
+
+        * gene - gene: red
+        * stimulus - stimulus: blue (deprecated)
+        * gene - stimulus: red
+        * molecule of interest - stimulus: yellow
+
+    :Legend of the nodes:
+
+        * genes: red
+        * stimuli: blue
+        * molecules of interest: yellow
+
+    :param all_genes: All genes in all the solutions
+    :param all_stimuli: All stimulis in all the solutions
+    :param genes_interactions: Interactions between genes in the same solution
+    :param stimulis_interactions: Interactions between stimuli in the same solution
+    :param genes_stimuli_interactions: Interactions between genes and stimulis in
+        the same solution
+    :param molecule_stimuli_interactions: Counter interactions between molecules
+        of interest and frontier places that are not genes (stimuli)
+        in trajectories (i.e.: ``(molecule, stimulus)``).
+    :type all_genes: <set>
+    :type all_stimuli: <set>
+    :type genes_interactions: <Counter>
+    :type stimulis_interactions: <Counter>
+    :type genes_stimuli_interactions: <Counter>
+    :type molecule_stimuli_interactions: <Counter>
     """
 
-    # Counter update...
+    # Count all nodes
     nodes_count = Counter(it.chain(*unique_genes_interactions.keys()))
     nodes_count.update(it.chain(*unique_stimulis_interactions.keys()))
     nodes_count.update(it.chain(*unique_genes_stimuli_interactions.keys()))
     nodes_count.update(it.chain(*unique_molecule_stimuli_interactions.keys()))
 
-
-    import networkx as nx
     # Make Graph ###############################################################
     def colormap(node):
         if node in all_genes:
@@ -380,6 +417,8 @@ def build_graph(all_genes, all_stimuli, unique_genes_interactions,
     def build_edge_data(edges):
         return [(node1, node2, weight) for (node1, node2), weight in edges.iteritems()]
 
+    # Add all edges
+    # PS Syntax: G.add_weighted_edges_from([(0,1,3.0),(1,2,7.5)],color='red')
     # Interactions between genes in the same solution
     G.add_weighted_edges_from(
         build_edge_data(unique_genes_interactions), color='red')
@@ -390,9 +429,11 @@ def build_graph(all_genes, all_stimuli, unique_genes_interactions,
         build_edge_data(unique_genes_stimuli_interactions), color='red')
     # Interactions between molecules of interest and frontier places that are not genes in trajectories
     G.add_weighted_edges_from(
-        build_edge_data(unique_filtered_binary_interactions), color='yellow')
+        build_edge_data(unique_molecule_stimuli_interactions), color='yellow')
+
+    # Write graph
+    nx.write_graphml(G, "test.graphml")
 
-#    G.add_weighted_edges_from([(0,1,3.0),(1,2,7.5)],color='red')
 
 
     nx.write_graphml(G, "test.graphml")