Source code for padmet_utils.exploration.visu_path

# -*- coding: utf-8 -*-
    #TODO: not stable version
    Allows to visualize a pathway in padmet network.
Color code: 
reactions associated to the pathway, present in the network: lightGreen
reactions associated to the pathway, not present in the network: red
compounds: skyblue


    usage: --padmetSpec=FILE --padmetRef=FILE --pathway=ID
        -h --help     Show help.
        --padmetSpec=FILE    pathname to the PADMet file of the network.
        --padmetRef=FILE    pathname to the PADMet file of the db of reference.
        --pathway=ID    pathway id to visualize.

from padmet.classes import PadmetRef, PadmetSpec
import networkx as nx
from networkx.drawing.nx_agraph import graphviz_layout
import matplotlib.pylab as plt
import docopt

[docs]def main(): args = docopt.docopt(__doc__) padmet_ref = PadmetRef(args["--padmetRef"]) padmet = PadmetSpec(args["--padmetSpec"]) pathway_id = args["--pathway"] #get all reactions in pathway try: all_reactions = [rlt.id_in for rlt in padmet_ref.dicOfRelationOut.get(pathway_id,None) if rlt.type == "is_in_pathway"] except TypeError: print("%s not in padmetRef" %pathway_id) exit() reactions_in_network = [] for reaction_id in all_reactions: try: padmet.dicOfNode[reaction_id] reactions_in_network.append(reaction_id) except KeyError: pass DG=nx.DiGraph() custom_node_color = {} for reaction_id in all_reactions: # Reaction colors if reaction_id in reactions_in_network: custom_node_color[reaction_id] = "lightgreen" else: custom_node_color[reaction_id] = "red" # Reactants & products for each reaction reactants = [rlt.id_out for rlt in padmet_ref.dicOfRelationIn.get(reaction_id, None) if rlt.type == "consumes"] products = [rlt.id_out for rlt in padmet_ref.dicOfRelationIn.get(reaction_id, None) if rlt.type == "produces"] for reac in reactants: custom_node_color[reac] = "skyblue" DG.add_edge(reac, reaction_id) for prod in products: custom_node_color[prod] = "skyblue" DG.add_edge(reaction_id, prod) # # apt-get install graphviz graphviz-dev (python-pygraphviz) # pip install pygraphviz nx.draw_networkx(DG, pos=graphviz_layout(DG, prog='neato'), # Layout from graphviz node_size=1600, arrows=True, font_size=11, # font-size for labels node_shape='s', # shape of nodes alpha=0.6, # node & edge transparency width=1.5, # line width for edges node_list=list(custom_node_color.keys()), node_color=list(custom_node_color.values())) plt.axis('off') #save_plot(plt, 'pathway_' + pathway_id)
[docs]def save_plot(plot, filepath): """Saves plot in multiple formats :param arg1: plot object :param arg2: filename with its path :type arg1: <plot object> :type arg2: <str> """ plot.savefig(filepath + ".png", dpi=144, format='png') plot.savefig(filepath + ".svg", dpi=144, format='svg')
#plot.savefig(filepath + ".pdf", # dpi=144, format='pdf') if __name__ == "__main__": main()