diff rpviz/nxvisualizer.py @ 16:fe78fd6b315a draft

planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpviz/nxvisualizer.py	Tue Jun 11 11:42:40 2019 -0400
@@ -0,0 +1,139 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu May 30 10:21:48 2019
+
+@author: anael
+"""
+#Usefull
+import inspect
+#inspect.getargspec(function)
+
+import networkx as nx
+from IPython.display import Image
+import requests
+import json
+import pandas as pd
+
+# Library for util
+from py2cytoscape.data.cynetwork import CyNetwork
+from py2cytoscape.data.cyrest_client import CyRestClient
+from py2cytoscape.data.style import StyleUtil
+
+
+def network(LR,Lreact,Lprod,name,smile,image):
+    ###Create the network with networkx
+    G=nx.DiGraph()
+    G.add_nodes_from(LR) #add reactions nodes
+    
+    
+    for i in range(len(LR)):
+        for j in range(len(Lreact[i])):
+            G.add_edge(Lreact[i][j],LR[i]) #add reactants nodes
+        for k in range(len(Lprod[i])):
+            G.add_edge(LR[i],Lprod[i][k]) #add products nodes
+    
+    #Attribute category
+    
+    dic_types={}
+    for i in range(len(LR)):
+        dic_types[(list(G.nodes))[i]]='reactions'
+        for node in range(len(list(G.nodes))):
+            if list(G.nodes)[node] in Lprod[i]:
+                dic_types[list(G.nodes)[node]]='product'
+            if list(G.nodes)[node] not in dic_types:
+                dic_types[list(G.nodes)[node]]='reactant'
+    print(dic_types)
+    nx.set_node_attributes(G,name='category',values=dic_types)
+    
+    #Attribute smile
+    nx.set_node_attributes(G, name='smiles', values=smile)
+    
+    #Attribute image
+    nx.set_node_attributes(G,name='image', values=image)
+
+    nx.write_gml(G,name+'.gml')
+    
+    #Connect with cytoscape
+    cy = CyRestClient()
+    
+    # Reset
+    #cy.session.delete()
+    
+    #To create the network in cytoscape
+    network = cy.network.create_from_networkx(G, name=name, collection='My network collection')
+    print('New network created with py2cytoscape.  Its SUID is ' + str(network.get_id()))
+    
+    #To get the SUID of all the components of the network
+    all_suid = cy.network.get_all()
+    net1 = cy.network.create(all_suid[0])
+    print(net1.get_first_view())
+    
+    #Styles
+    cy.layout.apply(name='hierarchical', network=network)
+    
+    # Get all existing Visual Styles
+    styles = cy.style.get_all()
+    print(json.dumps(styles, indent=4))
+    
+    
+    # Get a reference to the existing style
+    default_style = cy.style.create('default')
+    print(default_style.get_name())
+    
+    # Get all available Visual Properties
+    print(len(cy.style.vps.get_all()))
+    node_vps=cy.style.vps.get_node_visual_props()
+    edge_vps = cy.style.vps.get_edge_visual_props()
+    network_vps=cy.style.vps.get_network_visual_props()
+    print(pd.Series(edge_vps).head())
+    print(pd.Series(node_vps).head())
+    
+    
+    # Create a new style
+    style1 = cy.style.create("My_style")
+    print(style1.get_name())
+    
+    
+    new_defaults = {
+        # Node defaults
+        'NODE_FILL_COLOR': '#00ddee',
+        'NODE_SIZE': 20,
+        'NODE_BORDER_WIDTH': 0,
+        'NODE_LABEL_COLOR': 'black',
+        
+        # Edge defaults
+        'EDGE_WIDTH': 3,
+        'EDGE_STROKE_UNSELECTED_PAINT': '#aaaaaa',
+        'EDGE_LINE_TYPE': 'LONG_DASH',
+        'EDGE_TARGET_ARROW_SHAPE' : 'DELTA',
+        
+        # Network defaults
+        'NETWORK_BACKGROUND_PAINT': 'white',
+    }
+    
+    style1.update_defaults(new_defaults)
+    #Apply style
+    cy.style.apply(style1, network)
+    
+    # Passthrough mapping to get node labels
+    style1.create_passthrough_mapping(column='name', col_type='String', vp='NODE_LABEL')
+    
+    # Discrete mapping for node colours:
+    cat = {
+        'reactant': '#4D833C',
+        'product': '#C04E5D'
+    }
+    style1.create_discrete_mapping(column='category', 
+                                   col_type='String', 
+                                   vp='NODE_FILL_COLOR', 
+                                   mappings=cat)
+    
+    # Discrete mapping for node shape:
+    reac = {
+        'reactions': 'RECTANGLE'
+    }
+    style1.create_discrete_mapping(column='category', 
+                                   col_type='String', 
+                                   vp='NODE_SHAPE', 
+                                   mappings=reac)
+