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
