for e in geneSet: for g in e.graphics: if g.type == 'line': g.fgcolor = color g.width = width g.bgcolor = color #main enhanceSet = knownKOSet #notDE = set([e for e in pathway.entries.values() if not len(set(e.name.split()).intersection(enhanceSet)) and e.type != 'map']) notDE = set([e for e in pathway.orthologs if not len(set(e.name.split()).intersection(enhanceSet))]) kgml_map = KGMLCanvas(pathway, show_maps=True) kgml_map.import_imagemap = True #kgml_map.show_maps = False kgml_map.show_orthologs = True kgml_map.draw_relations = False kgml_map.show_compounds = False kgml_map.show_genes = False colorMapItems(notDE,'#D3D3D3', 1) os.chdir(args.outDir) koInMap = open(args.path + '_KO.txt', 'w') colorMapItems(knownKOSet,'#666666', 10) for k in knownKOSet: koInMap.write(k.name + '\t' + 'present' + '\n') koInMap.close() # And rendering elements as an overlay #kgml_map.show_compounds = True
knownKOSet = readKOFile(args.transKO, pathway) enhanceSet = knownKOSet if args.upKO != None: upKOSet = readKOFile(args.upKO, pathway) enhanceSet.update(upKOSet) if args.downKO != None: downKOSet = readKOFile(args.downKO, pathway) enhanceSet.update(downKOSet) notDE = set([e for e in pathway.orthologs if not len(set(e.name.split()).intersection(enhanceSet))]) kgml_map = KGMLCanvas(pathway, show_maps=True) kgml_map.import_imagemap = True # turn this off to allow all elements to go gray! kgml_map.show_maps = False kgml_map.show_orthologs = False kgml_map.draw_relations = False kgml_map.show_compounds = False kgml_map.show_genes = False os.chdir(args.outDir) colorMapItems(notDE,'#D3D3D3', 1) colorMapItems(knownKOSet,'#666666', 10) if args.upKO != None: colorMapItems(upKOSet,'#FF0000', 10) if args.downKO != None: colorMapItems(downKOSet,'#0000FF', 10) # And rendering elements as an overlay
if args.upKO != None: upKOSet = readKOFile(args.upKO, pathway) enhanceSet.update(upKOSet) if args.downKO != None: downKOSet = readKOFile(args.downKO, pathway) enhanceSet.update(downKOSet) notDE = set([ e for e in pathway.orthologs if not len(set(e.name.split()).intersection(enhanceSet)) ]) kgml_map = KGMLCanvas(pathway, show_maps=True) kgml_map.import_imagemap = True # turn this off to allow all elements to go gray! kgml_map.show_maps = False kgml_map.show_orthologs = False kgml_map.draw_relations = False kgml_map.show_compounds = False kgml_map.show_genes = False os.chdir(args.outDir) colorMapItems(notDE, '#D3D3D3', 1) colorMapItems(knownKOSet, '#666666', 10) if args.upKO != None: colorMapItems(upKOSet, '#FF0000', 10) if args.downKO != None: colorMapItems(downKOSet, '#0000FF', 10) # And rendering elements as an overlay