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
예제 #2
0
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
예제 #3
0
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