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A bug is fixed for domain colors.
A new parameter (-pdt) to be able to remove (use 0, default:1) dashed
lines when plotting domains with the in-built TAD caller.
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@akdemirlab
akdemirlab committed May 26, 2016
1 parent a70d58f commit 0af9ac9
Showing 1 changed file with 15 additions and 13 deletions.
28 changes: 15 additions & 13 deletions HiCPlotter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@
import bisect
import logging

version = "0.6.1.compare"
version = "0.6.2.compare"

def read_HiCdata(filename,header=0,footer=0,clean_nans=True,smooth_noise=0.5,ins_window=5,rel_window=8,plotInsulation=True,plotTadDomains=False,randomBins=False):

Expand Down Expand Up @@ -408,7 +408,7 @@ def insulation(matrix,w=5,tadRange=10):

def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histograms=[],histLabels=[],fillHist=[],histMax=[],verbose=False,fileHeader=0,fileFooter=0,matrixMax=0,histColors=[],barPlots=[],barLabels=[],\
start=0,end=0,tileLabels=[],tilePlots=[],tileColors=[],tileText=False,arcLabels=[],arcPlots=[],arcColors=[],peakFiles=[],epiLogos='',window=5,tadRange=8,tripleColumn=False,bedFile='',barColors=[],\
smoothNoise=0.5,cleanNANs=True,plotTriangular=True,plotTadDomains=False,randomBins=False,wholeGenome=False,plotPublishedTadDomains=False,plotDomainsAsBars=False,imputed=False,barMax=[],spine=False,\
smoothNoise=0.5,cleanNANs=True,plotTriangular=True,plotTadDomains=False,randomBins=False,wholeGenome=False,plotPublishedTadDomains=False,plotDomainsAsBars=False,imputed=False,barMax=[],spine=False,plotDomainTicks=True,\
highlights=0,highFile='',heatmapColor=3,highResolution=True,plotInsulation=True,plotCustomDomains=False,publishedTadDomainOrganism=True,customDomainsFile=[],compare=False,pair=False,domColors=[],oExtension=''):

'''
Expand Down Expand Up @@ -599,7 +599,8 @@ def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histo

if wholeGenome : plt.setp(ax1.get_yticklabels(), visible=False)
ax1.get_yaxis().set_label_coords(-0.125,0.5)
if plotTadDomains:

if plotTadDomains and plotDomainTicks:
ax1.set_xticks(tricks, minor=True)
ax1.xaxis.grid(True,which='minor',linewidth=2)

Expand Down Expand Up @@ -649,7 +650,7 @@ def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histo
plt.setp(ax2.get_yticklabels(), visible=False)
if exp==0: ax2.set_ylabel('Triangular')
ax2.get_yaxis().set_label_coords(-0.125,0.5)
if plotTadDomains:
if plotTadDomains and plotDomainTicks:
ax2.set_xticks(tricks, minor=True)
ax2.xaxis.grid(True,which='minor',linewidth=2)
rowcounter+=1
Expand Down Expand Up @@ -715,7 +716,7 @@ def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histo
with np.errstate(all='ignore'):ax3.fill_between(x_comps, comps2, 0, where=comps2<0, color='black', interpolate=True)

x_comps=[];x_comps2=[];y_comps=[];colors==[];
if plotTadDomains:
if plotTadDomains and plotDomainTicks:
ax3.set_xticks(tricks, minor=True)
ax3.xaxis.grid(True,which='minor')

Expand Down Expand Up @@ -758,7 +759,7 @@ def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histo
ax3.set_xlim(int(start or 1) - 0.5,int(start or 1) + length - 0.5)
ax3.set_ylim(0,hMax+hMax/10)
ax3.locator_params(axis='y',tight=False, nbins=4)
if plotTadDomains:
if plotTadDomains and plotDomainTicks:
ax3.set_xticks(tricks, minor=True)
ax3.xaxis.grid(True,which='minor')

Expand Down Expand Up @@ -797,7 +798,7 @@ def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histo
ax3.set_xlim(int(start or 1) - 0.5,int(start or 1) + length - 0.5)
ax3.set_ylim(0,1)
plt.setp(ax3.get_yticklabels(), visible=False)
if plotTadDomains:
if plotTadDomains and plotDomainTicks:
ax3.set_xticks(tricks, minor=True)
ax3.xaxis.grid(True,which='minor')

Expand Down Expand Up @@ -839,7 +840,7 @@ def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histo
ax3.set_xlim(int(start or 1) - 0.5,int(start or 1) + length - 0.5)
ax3.set_ylim(0,1)
plt.setp(ax3.get_yticklabels(), visible=False)
if plotTadDomains:
if plotTadDomains and plotDomainTicks:
ax3.set_xticks(tricks, minor=True)
ax3.xaxis.grid(True,which='minor')

Expand Down Expand Up @@ -909,7 +910,7 @@ def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histo
ax4.set_xlim(int(start or 1) - 0.5,int(start or 1) + length - 0.5)
ax4.plot(range(0,len(nums)),nums,'black')
ax4.fill_between(range(0,len(nums)),nums,0,color='0.8')
if plotTadDomains:
if plotTadDomains and plotDomainTicks:
ax4.set_xticks(tricks, minor=True)
ax4.xaxis.grid(True,which='minor')

Expand All @@ -934,9 +935,9 @@ def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histo
ax5 = plt.subplot2grid((numOfrows,4*len(files)), (rowcounter, exp*4), rowspan=1,colspan=4,sharex=ax1)

for item in range(0,len(tricks)-1):

tcolor='darkkhaki'
if len(colors)>0: tcolor=colors[item]
elif len(domColors)>0: tcolor='#'+domColors[exp]
if len(domColors)>0: tcolor='#'+domColors[exp]

if plotDomainsAsBars:
if not plotPublishedTadDomains: p = Rectangle((tricks[item],0.2), (tricks[item+1]-tricks[item]), 0.25, color=tcolor,alpha=0.75)
Expand Down Expand Up @@ -1216,7 +1217,7 @@ def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histo

if wholeGenome : plt.setp(ax1.get_yticklabels(), visible=False)
ax1.get_yaxis().set_label_coords(-0.125,0.5)
if plotTadDomains:
if plotTadDomains and plotDomainTicks:
ax1.set_xticks(tricks, minor=True)
ax1.xaxis.grid(True,which='minor',linewidth=2)

Expand Down Expand Up @@ -1289,7 +1290,7 @@ def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histo

if wholeGenome : plt.setp(pax1.get_yticklabels(), visible=False)
pax1.get_yaxis().set_label_coords(-0.125,0.5)
if plotTadDomains:
if plotTadDomains and plotDomainTicks:
pax1.set_xticks(tricks, minor=True)
pax1.xaxis.grid(True,which='minor',linewidth=2)

Expand Down Expand Up @@ -1397,6 +1398,7 @@ def HiCplotter(files=[],names=[],resolution=100000,chromosome='',output='',histo
group1.add_argument('-dc', '--domColors', nargs='+',metavar='',default=[])
group1.add_argument('-ptr', '--plotTriangular',type=int,default=False,metavar='',help="default: 1 - disable with 0")
group1.add_argument('-ptd', '--plotTadDomains',type=int,default=False,metavar='',help="default: 0 - enable with 1")
group1.add_argument('-pdt', '--plotDomainTicks',type=int,default=True,metavar='',help="default: 1 - enable with 0")
group1.add_argument('-pcd', '--plotCustomDomains',type=int,default=False,metavar='',help="default: 0 - enable with 1")
group1.add_argument('-pdb', '--plotDomainsAsBars',type=int,default=False,metavar='',help="default: 0 - enable with 1")
group1.add_argument('-pcdf', '--customDomainsFile',nargs='+',metavar='',default=[])
Expand Down

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