Mercurial > repos > pablocarb > synbiodesign
view rpviz/nxvisualizer.py @ 29:d854b21ada0c draft
planemo upload commit c56eddc745b70354680c2a2b605840ed72bb98ef
author | pablocarb |
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date | Wed, 07 Aug 2019 05:13:27 -0400 |
parents | fe78fd6b315a |
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# -*- 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)