def drawThreeVenn(set1,set2,set3,set1set2Intersect,set1set3Intersect,set2set3Intersect,allIntersect,width,height,outfile,title=None,legend=None,indicateNumberInLegend=False,colors=None,htmlReport=None):
chart=VennChart(width,height)
chart.add_data([set1,set2,set3,set1set2Intersect,set1set3Intersect,set2set3Intersect,allIntersect])
if title:
chart.set_title(title)
if legend:
legendOut=legend[:]
if indicateNumberInLegend:
legendOut[0]=legend[0]+" ("+str(set1)+")"
legendOut[1]=legend[1]+" ("+str(set2)+")"
legendOut[2]=legend[2]+" ("+str(set3)+")"
chart.set_legend(legendOut)
if colors:
for i in range(0,len(colors)):
if type(colors[i]) is not StringType:
#probably a int tuple (4 or 3)
#print >> stderr,colors[i],"is not string"
if type(colors[i]) is ListType or type(colors[i]) is TupleType:
#print >> stderr,"is list or tuple"
hexCode=""
for color_component in colors[i]:
hexCode+=twodigithex(color_component)
colors[i]=hexCode
#print >> stderr,colors
chart.set_colours(colors)
chart.download(outfile)
if htmlReport:
fout = open(htmlReport,"w")
set1only=set1-set1set2Intersect-set1set3Intersect+allIntersect
set2only=set2-set1set2Intersect-set2set3Intersect+allIntersect
set3only=set3-set1set3Intersect-set2set3Intersect+allIntersect
if not title:
title=""
if not legend:
legend=["set1","set2","set3"]
print >> fout, '<html><head><title>%s</title></head><body><h1>%s</h1><table width=%d><tr><td colspan=2><img src="%s"></td></tr><tr bgcolor="#AAAAAA"><td>%s</td><td>%d</td></tr><tr><td>%s</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>%s</td><td>%d</td></tr> <tr> <td>%s only</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>%s only</td><td>%d</td> </tr> <tr><td>%s only</td><td>%d</td> </tr> <tr bgcolor="#AAAAAA"> <td>%s ∩ %s</td><td>%d</td></tr> <tr> <td>%s ∩ %s</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>%s ∩ %s</td><td>%d</td></tr> <tr> <td>%s ∩ %s ∩ %s </td><td>%d</td></tr> </body></html>' %(title,title,width,basename(outfile),legend[0],set1,legend[1],set2,legend[2],set3,legend[0],set1only,legend[1],set2only,legend[2],set3only,legend[0],legend[1],set1set2Intersect,legend[0],legend[2],set1set3Intersect,legend[1],legend[2],set2set3Intersect,legend[0],legend[1],legend[2],allIntersect)
fout.close()
def drawTwoVenn(set1,
set2,
intersect,
width,
height,
outfile,
fisherU=None,
title=None,
legend=None,
indicateNumberInLegend=False,
colors=None,
htmlReport=None):
chart = VennChart(width, height)
chart.add_data([set1, set2, 0, intersect])
if title:
chart.set_title(title)
if legend:
legendOut = legend[:]
if indicateNumberInLegend:
legendOut[0] = legend[0] + " (" + str(set1) + ")"
legendOut[1] = legend[1] + " (" + str(set2) + ")"
chart.set_legend(legendOut)
if colors:
for i in range(0, len(colors)):
if type(colors[i]) is not StringType:
#probably a int tuple (4 or 3)
#print >> stderr,colors[i],"is not string"
if type(colors[i]) is ListType or type(colors[i]) is TupleType:
#print >> stderr,"is list or tuple"
hexCode = ""
for color_component in colors[i]:
hexCode += twodigithex(color_component)
colors[i] = hexCode
#print >> stderr,colors
chart.set_colours(colors)
chart.download(outfile)
if fisherU:
#build a contingency table 2x2
box1 = intersect
box2 = set2 - intersect
box3 = set2
box6 = fisherU - set2
box7 = set1
box8 = fisherU - set1
box9 = fisherU
box4 = set1 - intersect
box5 = fisherU - set1 - set2 + intersect
fisher_pvalues = fisher.pvalue(box1, box2, box4, box5)
expectedIntersect = round(float(set1) * set2 / fisherU)
if htmlReport:
if not title:
title = ""
if not legend:
legend = ["set1", "set2"]
fout = open(htmlReport, "w")
print >> fout, '<html><head><title>%s</title></head><body><h1>%s</h1><table width=%d><tr><td colspan=2><img src="%s"></td></tr><tr bgcolor="#AAAAAA"><td>%s</td><td>%d</td></tr><tr><td>%s</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>%s only</td><td>%d</td></tr> <tr><td>%s only</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>%s ∩ %s</td><td>%d</td></tr> ' % (
title, title, width, basename(outfile), legend[0], set1, legend[1],
set2, legend[0], set1 - intersect, legend[1], set2 - intersect,
legend[0], legend[1], intersect)
if fisherU:
print >> fout, '<tr><td>Universe</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>E[%s ∩ %s]</td><td>%d</td></tr> <tr><td>dnrichment p-value</td><td>%g</td></tr> <tr bgcolor="#AAAAAA"> <td>depletion p-value</td><td>%g</td></tr>' % (
fisherU, legend[0], legend[1], expectedIntersect,
fisher_pvalues.right_tail, fisher_pvalues.left_tail)
print >> fout, '</body></html>'
fout.close()
def drawTwoVenn(set1,set2,intersect,width,height,outfile,fisherU=None,title=None,legend=None,indicateNumberInLegend=False,colors=None,htmlReport=None):
chart=VennChart(width,height)
chart.add_data([set1,set2,0,intersect])
if title:
chart.set_title(title)
if legend:
legendOut=legend[:]
if indicateNumberInLegend:
legendOut[0]=legend[0]+" ("+str(set1)+")"
legendOut[1]=legend[1]+" ("+str(set2)+")"
chart.set_legend(legendOut)
if colors:
for i in range(0,len(colors)):
if type(colors[i]) is not StringType:
#probably a int tuple (4 or 3)
#print >> stderr,colors[i],"is not string"
if type(colors[i]) is ListType or type(colors[i]) is TupleType:
#print >> stderr,"is list or tuple"
hexCode=""
for color_component in colors[i]:
hexCode+=twodigithex(color_component)
colors[i]=hexCode
#print >> stderr,colors
chart.set_colours(colors)
chart.download(outfile)
if fisherU:
#build a contingency table 2x2
box1=intersect
box2=set2-intersect
box3=set2
box6=fisherU-set2
box7=set1
box8=fisherU-set1
box9=fisherU
box4=set1-intersect
box5=fisherU-set1-set2+intersect
fisher_pvalues=fisher.pvalue(box1,box2,box4,box5)
expectedIntersect=round(float(set1)*set2/fisherU)
if htmlReport:
if not title:
title=""
if not legend:
legend=["set1","set2"]
fout = open(htmlReport,"w")
print >> fout, '<html><head><title>%s</title></head><body><h1>%s</h1><table width=%d><tr><td colspan=2><img src="%s"></td></tr><tr bgcolor="#AAAAAA"><td>%s</td><td>%d</td></tr><tr><td>%s</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>%s only</td><td>%d</td></tr> <tr><td>%s only</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>%s ∩ %s</td><td>%d</td></tr> ' %(title,title,width,basename(outfile),legend[0],set1,legend[1],set2,legend[0],set1-intersect,legend[1],set2-intersect,legend[0],legend[1],intersect)
if fisherU:
print >> fout, '<tr><td>Universe</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>E[%s ∩ %s]</td><td>%d</td></tr> <tr><td>dnrichment p-value</td><td>%g</td></tr> <tr bgcolor="#AAAAAA"> <td>depletion p-value</td><td>%g</td></tr>' %(fisherU,legend[0],legend[1],expectedIntersect,fisher_pvalues.right_tail,fisher_pvalues.left_tail)
print >> fout, '</body></html>'
fout.close()
def drawThreeVenn(set1,
set2,
set3,
set1set2Intersect,
set1set3Intersect,
set2set3Intersect,
allIntersect,
width,
height,
outfile,
title=None,
legend=None,
indicateNumberInLegend=False,
colors=None,
htmlReport=None):
chart = VennChart(width, height)
chart.add_data([
set1, set2, set3, set1set2Intersect, set1set3Intersect,
set2set3Intersect, allIntersect
])
if title:
chart.set_title(title)
if legend:
legendOut = legend[:]
if indicateNumberInLegend:
legendOut[0] = legend[0] + " (" + str(set1) + ")"
legendOut[1] = legend[1] + " (" + str(set2) + ")"
legendOut[2] = legend[2] + " (" + str(set3) + ")"
chart.set_legend(legendOut)
if colors:
for i in range(0, len(colors)):
if type(colors[i]) is not StringType:
#probably a int tuple (4 or 3)
#print >> stderr,colors[i],"is not string"
if type(colors[i]) is ListType or type(colors[i]) is TupleType:
#print >> stderr,"is list or tuple"
hexCode = ""
for color_component in colors[i]:
hexCode += twodigithex(color_component)
colors[i] = hexCode
#print >> stderr,colors
chart.set_colours(colors)
chart.download(outfile)
if htmlReport:
fout = open(htmlReport, "w")
set1only = set1 - set1set2Intersect - set1set3Intersect + allIntersect
set2only = set2 - set1set2Intersect - set2set3Intersect + allIntersect
set3only = set3 - set1set3Intersect - set2set3Intersect + allIntersect
if not title:
title = ""
if not legend:
legend = ["set1", "set2", "set3"]
print >> fout, '<html><head><title>%s</title></head><body><h1>%s</h1><table width=%d><tr><td colspan=2><img src="%s"></td></tr><tr bgcolor="#AAAAAA"><td>%s</td><td>%d</td></tr><tr><td>%s</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>%s</td><td>%d</td></tr> <tr> <td>%s only</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>%s only</td><td>%d</td> </tr> <tr><td>%s only</td><td>%d</td> </tr> <tr bgcolor="#AAAAAA"> <td>%s ∩ %s</td><td>%d</td></tr> <tr> <td>%s ∩ %s</td><td>%d</td></tr> <tr bgcolor="#AAAAAA"> <td>%s ∩ %s</td><td>%d</td></tr> <tr> <td>%s ∩ %s ∩ %s </td><td>%d</td></tr> </body></html>' % (
title, title, width, basename(outfile), legend[0], set1, legend[1],
set2, legend[2], set3, legend[0], set1only, legend[1], set2only,
legend[2], set3only, legend[0], legend[1], set1set2Intersect,
legend[0], legend[2], set1set3Intersect, legend[1], legend[2],
set2set3Intersect, legend[0], legend[1], legend[2], allIntersect)
fout.close()