def CF_plot(args):
try:
import locale
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pylab as P
from matplotlib.lines import Line2D
from matplotlib.patches import Rectangle
_ = locale.setlocale(locale.LC_ALL, '')
except:
print "[ERROR] One or more of the required modules for plotting cannot be loaded! Are matplotlib and pylab installed?"
sys.exit(0)
chr, start, stop = cf.parseLocString(args.region)
r = cf.rpkm_reader(args.input)
data = r.getExonValuesByRegion(chr,start,stop)
_ = data.smooth()
plt.gcf().clear()
fig = plt.figure(figsize=(10,5))
ax = fig.add_subplot(111)
ax.plot(data.rpkm, linewidth = 0.3, c='k')
if args.sample != 'none':
cnt = 1
coloriter = iter(['r','b','g','y'])
for sample in args.sample:
try:
color, sampleID = sample.split(":")
except:
color =coloriter.next()
sampleID = sample
ax.plot(data.getSample([sampleID]), linewidth = 1, c=color, label = sampleID)
if cnt == 1:
cf.plotRawData(ax, r.getExonValuesByRegion(chr,start,stop,sampleList=[sampleID]).getSample([sampleID]),color=color)
cnt +=1
plt.legend(prop={'size':10},frameon=False)
cf.plotGenes(ax, data)
cf.plotGenomicCoords(plt,data)
plt.xlim(0,data.shape[1])
plt.ylim(-3,3)
plt.title("%s: %s - %s" % (cf.chrInt2Str(chr),locale.format("%d",start, grouping=True),locale.format("%d",stop, grouping=True)))
plt.xlabel("Position")
plt.ylabel("SVD-ZRPKM Values")
plt.savefig(args.output)
sys.exit(0)
def CF_plot(args):
try:
import locale
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pylab as P
from matplotlib.lines import Line2D
from matplotlib.patches import Rectangle
_ = locale.setlocale(locale.LC_ALL, '')
except:
print "[ERROR] One or more of the required modules for plotting cannot be loaded! Are matplotlib and pylab installed?"
sys.exit(0)
chr, start, stop = cf.parseLocString(args.region)
r = cf.rpkm_reader(args.input)
data = r.getExonValuesByRegion(chr,start,stop)
_ = data.smooth()
plt.gcf().clear()
fig = plt.figure(figsize=(10,5))
ax = fig.add_subplot(111)
ax.plot(data.rpkm, linewidth = 0.3, c='k')
if args.sample != 'none':
cnt = 1
coloriter = iter(['r','b','g','y'])
for sample in args.sample:
try:
color, sampleID = sample.split(":")
except:
color =coloriter.next()
sampleID = sample
ax.plot(data.getSample([sampleID]), linewidth = 1, c=color, label = sampleID)
if cnt == 1:
cf.plotRawData(ax, r.getExonValuesByRegion(chr,start,stop,sampleList=[sampleID]).getSample([sampleID]),color=color)
cnt +=1
plt.legend(prop={'size':10},frameon=False)
cf.plotGenes(ax, data)
cf.plotGenomicCoords(plt,data)
plt.xlim(0,data.shape[1])
plt.ylim(-3,3)
plt.title("%s: %s - %s" % (cf.chrInt2Str(chr),locale.format("%d",start, grouping=True),locale.format("%d",stop, grouping=True)))
plt.xlabel("Position")
plt.ylabel("SVD-ZRPKM Values")
plt.savefig(args.output)
sys.exit(0)