def buildCanvas(self, colorScheme='', targetDescriptionChecked='', clusterChecked='', sessionfile='', genotype=None, strainlist=None, ppolar=None, mpolar=None, traitList=None, traitDataList=None, userPrivilege=None, userName=None):
labelFont = pid.Font(ttf="tahoma",size=14,bold=0)
topHeight = 0
NNN = len(traitList)
#XZ: It's necessory to define canvas here
canvas = pid.PILCanvas(size=(80+NNN*20,880))
names = map(webqtlTrait.displayName, traitList)
#XZ, 7/29/2009: create trait display and find max strWidth
strWidth = 0
for j in range(len(names)):
thisTrait = traitList[j]
if targetDescriptionChecked:
if thisTrait.db.type == 'ProbeSet':
if thisTrait.probe_target_description:
names[j] += ' [%s at Chr %s @ %2.3fMB, %s]' % (thisTrait.symbol, thisTrait.chr, thisTrait.mb, thisTrait.probe_target_description)
else:
names[j] += ' [%s at Chr %s @ %2.3fMB]' % (thisTrait.symbol, thisTrait.chr, thisTrait.mb)
elif thisTrait.db.type == 'Geno':
names[j] += ' [Chr %s @ %2.3fMB]' % (thisTrait.chr, thisTrait.mb)
elif thisTrait.db.type == 'Publish':
if thisTrait.confidential:
if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=userPrivilege, userName=userName, authorized_users=thisTrait.authorized_users):
if thisTrait.post_publication_abbreviation:
names[j] += ' [%s]' % (thisTrait.post_publication_abbreviation)
else:
if thisTrait.pre_publication_abbreviation:
names[j] += ' [%s]' % (thisTrait.pre_publication_abbreviation)
else:
if thisTrait.post_publication_abbreviation:
names[j] += ' [%s]' % (thisTrait.post_publication_abbreviation)
else:
pass
i = canvas.stringWidth(names[j], font=labelFont)
if i > strWidth:
strWidth = i
width = NNN*20
xoffset = 40
yoffset = 40
cellHeight = 3
nLoci = reduce(lambda x,y: x+y, map(lambda x: len(x),genotype),0)
if nLoci > 2000:
cellHeight = 1
elif nLoci > 1000:
cellHeight = 2
elif nLoci < 200:
cellHeight = 10
else:
pass
pos = range(NNN)
neworder = []
BWs = Plot.BWSpectrum()
colors100 = Plot.colorSpectrum()
colors = Plot.colorSpectrum(130)
finecolors = Plot.colorSpectrum(250)
colors100.reverse()
colors.reverse()
finecolors.reverse()
scaleFont=pid.Font(ttf="tahoma",size=10,bold=0)
if not clusterChecked: #XZ: this part is for original order
for i in range(len(names)):
neworder.append((xoffset+20*(i+1), i))
canvas = pid.PILCanvas(size=(80+NNN*20+240,80+ topHeight +5+5+strWidth+nLoci*cellHeight+80+20*cellHeight))
self.drawTraitNameBottom(canvas,names,yoffset,neworder,strWidth,topHeight,labelFont)
else: #XZ: this part is to cluster traits
topHeight = 400
canvas = pid.PILCanvas(size=(80+NNN*20+240,80+ topHeight +5+5+strWidth+nLoci*cellHeight+80+20*cellHeight))
corArray = [([0] * (NNN))[:] for i in range(NNN)]
nnCorr = len(strainlist)
#XZ, 08/04/2009: I commented out pearsonArray, spearmanArray
for i, thisTrait in enumerate(traitList):
names1 = [thisTrait.db.name, thisTrait.name, thisTrait.cellid]
for j, thisTrait2 in enumerate(traitList):
names2 = [thisTrait2.db.name, thisTrait2.name, thisTrait2.cellid]
if j < i:
corr,nOverlap = webqtlUtil.calCorrelation(traitDataList[i], traitDataList[j],nnCorr)
if (1-corr) < 0:
distance = 0.0
else:
distance = 1-corr
corArray[i][j] = distance
corArray[j][i] = distance
elif j == i:
corArray[i][j] = 0.0
else:
pass
#XZ, 7/29/2009: The parameter d has info of cluster (group member and distance). The format of d is tricky. Print it out to see it's format.
d = slink.slink(corArray)
#XZ, 7/29/2009: Attention: The 'neworder' is changed by the 'draw' function
#XZ, 7/30/2009: Only toppos[1][0] and top[1][1] are used later. Then what toppos[0] is used for?
toppos = self.draw(canvas,names,d,xoffset,yoffset,neworder,topHeight)
self.drawTraitNameTop(canvas,names,yoffset,neworder,strWidth,topHeight,labelFont)
#XZ, 7/29/2009: draw the top vertical line
canvas.drawLine(toppos[1][0],toppos[1][1],toppos[1][0],yoffset)
#XZ: draw string 'distance = 1-r'
canvas.drawString('distance = 1-r',neworder[-1][0] + 50, topHeight*3/4,font=labelFont,angle=90)
#draw Scale
scaleFont=pid.Font(ttf="tahoma",size=10,bold=0)
x = neworder[-1][0]
canvas.drawLine(x+5, topHeight+yoffset, x+5, yoffset, color=pid.black)
y = 0
while y <=2:
canvas.drawLine(x+5, topHeight*y/2.0+yoffset, x+10, topHeight*y/2.0+yoffset)
canvas.drawString('%2.1f' % (2-y), x+12, topHeight*y/2.0+yoffset, font=scaleFont)
y += 0.5
chrname = 0
chrnameFont=pid.Font(ttf="tahoma",size=24,bold=0)
Ncol = 0
nearestMarkers = self.getNearestMarker(traitList, genotype)
# import cPickle
if sessionfile:
fp = open(os.path.join(webqtlConfig.TMPDIR, sessionfile + '.session'), 'rb')
permData = cPickle.load(fp)
fp.close()
else:
permData = {}
areas = []
#XZ, 7/31/2009: This for loop is to generate the heatmap
#XZ: draw trait by trait instead of marker by marker
for order in neworder:
#startHeight = 40+400+5+5+strWidth
startHeight = topHeight + 40+5+5+strWidth
startWidth = order[0]-5
if Ncol and Ncol % 5 == 0:
drawStartPixel = 8
else:
drawStartPixel = 9
tempVal = traitDataList[order[1]]
_vals = []
_strains = []
for i in range(len(strainlist)):
if tempVal[i] != None:
_strains.append(strainlist[i])
_vals.append(tempVal[i])
qtlresult = genotype.regression(strains = _strains, trait = _vals)
if sessionfile:
LRSArray = permData[str(traitList[order[1]])]
else:
LRSArray = genotype.permutation(strains = _strains, trait = _vals, nperm = 1000)
permData[str(traitList[order[1]])] = LRSArray
sugLRS = LRSArray[369]
sigLRS = LRSArray[949]
prechr = 0
chrstart = 0
nearest = nearestMarkers[order[1]]
midpoint = []
for item in qtlresult:
if item.lrs > webqtlConfig.MAXLRS:
adjustlrs = webqtlConfig.MAXLRS
else:
adjustlrs = item.lrs
if item.locus.chr != prechr:
if prechr:
canvas.drawRect(startWidth-drawStartPixel, startHeight, startWidth+10, startHeight+3,edgeColor=pid.white, edgeWidth=0, fillColor=pid.white)
startHeight+= 3
if not chrname:
canvas.drawString(prechr,xoffset-20,(chrstart+startHeight)/2,font = chrnameFont,color=pid.dimgray)
prechr = item.locus.chr
chrstart = startHeight
if colorScheme == '0':
if adjustlrs <= sugLRS:
colorIndex = int(65*adjustlrs/sugLRS)
else:
colorIndex = int(65 + 35*(adjustlrs-sugLRS)/(sigLRS-sugLRS))
if colorIndex > 99:
colorIndex = 99
colorIndex = colors100[colorIndex]
elif colorScheme == '1':
sugLRS = LRSArray[369]/2.0
if adjustlrs <= sugLRS:
colorIndex = BWs[20+int(50*adjustlrs/sugLRS)]
else:
if item.additive > 0:
colorIndex = int(80 + 50*(adjustlrs-sugLRS)/(sigLRS-sugLRS))
else:
colorIndex = int(50 - 50*(adjustlrs-sugLRS)/(sigLRS-sugLRS))
if colorIndex > 129:
colorIndex = 129
if colorIndex < 0:
colorIndex = 0
colorIndex = colors[colorIndex]
elif colorScheme == '2':
if item.additive > 0:
colorIndex = int(150 + 100*(adjustlrs/sigLRS))
else:
colorIndex = int(100 - 100*(adjustlrs/sigLRS))
if colorIndex > 249:
colorIndex = 249
if colorIndex < 0:
colorIndex = 0
colorIndex = finecolors[colorIndex]
else:
colorIndex = pid.white
if startHeight > 1:
canvas.drawRect(startWidth-drawStartPixel, startHeight, startWidth+10, startHeight+cellHeight,edgeColor=colorIndex, edgeWidth=0, fillColor=colorIndex)
else:
canvas.drawLine(startWidth-drawStartPixel, startHeight, startWidth+10, startHeight, Color=colorIndex)
if item.locus.name == nearest:
midpoint = [startWidth,startHeight-5]
startHeight+=cellHeight
#XZ, map link to trait name and band
COORDS = "%d,%d,%d,%d" %(startWidth-drawStartPixel,topHeight+40,startWidth+10,startHeight)
HREF = "javascript:showDatabase2('%s','%s','%s');" % (traitList[order[1]].db.name, traitList[order[1]].name, traitList[order[1]].cellid)
area = (COORDS, HREF, '%s' % names[order[1]])
areas.append(area)
if midpoint:
traitPixel = ((midpoint[0],midpoint[1]),(midpoint[0]-6,midpoint[1]+12),(midpoint[0]+6,midpoint[1]+12))
canvas.drawPolygon(traitPixel,edgeColor=pid.black,fillColor=pid.orange,closed=1)
if not chrname:
canvas.drawString(prechr,xoffset-20,(chrstart+startHeight)/2,font = chrnameFont,color=pid.dimgray)
chrname = 1
Ncol += 1
#draw Spectrum
startSpect = neworder[-1][0] + 30
startHeight = topHeight + 40+5+5+strWidth
if colorScheme == '0':
for i in range(100):
canvas.drawLine(startSpect+i,startHeight+20,startSpect+i,startHeight+40,color=colors100[i])
scaleFont=pid.Font(ttf="tahoma",size=10,bold=0)
canvas.drawLine(startSpect,startHeight+45,startSpect,startHeight+39,color=pid.black)
canvas.drawString('LRS = 0',startSpect,startHeight+55,font=scaleFont)
canvas.drawLine(startSpect+64,startHeight+45,startSpect+64,startHeight+39,color=pid.black)
canvas.drawString('Suggestive LRS',startSpect+64,startHeight+55,font=scaleFont)
canvas.drawLine(startSpect+99,startHeight+45,startSpect+99,startHeight+39,color=pid.black)
canvas.drawString('Significant LRS',startSpect+105,startHeight+40,font=scaleFont)
elif colorScheme == '1':
for i in range(50):
canvas.drawLine(startSpect+i,startHeight,startSpect+i,startHeight+40,color=BWs[20+i])
for i in range(50,100):
canvas.drawLine(startSpect+i,startHeight,startSpect+i,startHeight+20,color=colors[100-i])
canvas.drawLine(startSpect+i,startHeight+20,startSpect+i,startHeight+40,color=colors[30+i])
canvas.drawLine(startSpect,startHeight+45,startSpect,startHeight+39,color=pid.black)
canvas.drawString('LRS = 0',startSpect,startHeight+60,font=scaleFont)
canvas.drawLine(startSpect+50,startHeight+45,startSpect+50,startHeight+39,color=pid.black)
canvas.drawString('0.5*Suggestive LRS',startSpect+50,startHeight+ 60,font=scaleFont)
canvas.drawLine(startSpect+99,startHeight+45,startSpect+99,startHeight+39,color=pid.black)
canvas.drawString('Significant LRS',startSpect+105,startHeight+50,font=scaleFont)
textFont=pid.Font(ttf="verdana",size=18,bold=0)
canvas.drawString('%s +' % ppolar,startSpect+120,startHeight+ 35,font=textFont,color=pid.red)
canvas.drawString('%s +' % mpolar,startSpect+120,startHeight+ 15,font=textFont,color=pid.blue)
elif colorScheme == '2':
for i in range(100):
canvas.drawLine(startSpect+i,startHeight,startSpect+i,startHeight+20,color=finecolors[100-i])
canvas.drawLine(startSpect+i,startHeight+20,startSpect+i,startHeight+40,color=finecolors[150+i])
canvas.drawLine(startSpect,startHeight+45,startSpect,startHeight+39,color=pid.black)
canvas.drawString('LRS = 0',startSpect,startHeight+60,font=scaleFont)
canvas.drawLine(startSpect+99,startHeight+45,startSpect+99,startHeight+39,color=pid.black)
canvas.drawString('Significant LRS',startSpect+105,startHeight+50,font=scaleFont)
textFont=pid.Font(ttf="verdana",size=18,bold=0)
canvas.drawString('%s +' % ppolar,startSpect+120,startHeight+ 35,font=textFont,color=pid.red)
canvas.drawString('%s +' % mpolar,startSpect+120,startHeight+ 15,font=textFont,color=pid.blue)
filename= webqtlUtil.genRandStr("Heatmap_")
canvas.save(webqtlConfig.IMGDIR+filename, format='png')
if not sessionfile:
sessionfile = webqtlUtil.generate_session()
webqtlUtil.dump_session(permData, os.path.join(webqtlConfig.TMPDIR, sessionfile +'.session'))
self.filename=filename
self.areas=areas
self.sessionfile=sessionfile
def drawGraph(self, canvas, data, cLength = 2500, offset= (80, 160, 60, 60), XLabel="QTL location (GMb)", YLabel="Gene location (GMb)"):
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
#draw Frame
canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset)
#draw Scale
i = 100
scaleFont=pid.Font(ttf="cour",size=11,bold=1)
while i < cLength:
yCoord = plotHeight + yTopOffset - plotHeight*i/cLength
canvas.drawLine(xLeftOffset,yCoord ,xLeftOffset-5, yCoord)
canvas.drawString("%d"% i, xLeftOffset -40, yCoord +5,font=scaleFont)
xCoord = xLeftOffset + plotWidth*i/cLength
canvas.drawLine(xCoord, plotHeight + yTopOffset ,xCoord, plotHeight + yTopOffset+5)
canvas.drawString("%d"% i, xCoord -10, plotHeight + yTopOffset+15,font=scaleFont)
i += 100
#draw Points
finecolors = Plot.colorSpectrum(300)
finecolors.reverse()
for item in data:
_pvalue = item[-1]
try:
_idx = int((-math.log10(_pvalue))*300/6.0) # XZ, 09/11/2008: add module name
_color = finecolors[_idx]
except:
_color = finecolors[-1]
canvas.drawCross(xLeftOffset + plotWidth*item[0]/cLength, plotHeight + yTopOffset - plotHeight*item[1]/cLength, color=_color,size=3)
#draw grid / always draw grid
if 1: #self.grid == "on":
for key in self.mouseChrLengthDict.keys():
length = self.mouseChrLengthDict[key]
if length != 0:
yCoord = plotHeight + yTopOffset - plotHeight*length/cLength
canvas.drawLine(xLeftOffset,yCoord ,xLeftOffset+plotWidth, yCoord, color=pid.lightgrey)
xCoord = xLeftOffset + plotWidth*length/cLength
canvas.drawLine(xCoord, plotHeight + yTopOffset ,xCoord, yTopOffset, color=pid.lightgrey)
#draw spectrum
i = 0
j = 0
middleoffsetX = 40
labelFont=pid.Font(ttf="tahoma",size=12,bold=0)
for dcolor in finecolors:
canvas.drawLine(xLeftOffset+ plotWidth + middleoffsetX -15 , plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth + middleoffsetX+15 , plotHeight + yTopOffset - i, color=dcolor)
if i % 50 == 0:
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
canvas.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+5, font = labelFont)
j += 1
i += 1
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i+1, \
xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i+1, color=pid.black)
canvas.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+6, font = labelFont)
labelFont=pid.Font(ttf="tahoma",size=14,bold=1)
canvas.drawString("Log(pValue)" , xLeftOffset+ plotWidth +middleoffsetX+60 ,plotHeight + yTopOffset - 100, font = labelFont, angle =90)
labelFont=pid.Font(ttf="verdana",size=18,bold=0)
canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, plotHeight + yTopOffset +40, color=pid.blue, font=labelFont)
canvas.drawString(YLabel,xLeftOffset-60, plotHeight + yTopOffset-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0, color=pid.blue, font=labelFont, angle =90)
return
def __init__(self, fd):
LRSFullThresh = 30
LRSInteractThresh = 25
templatePage.__init__(self, fd)
if not fd.genotype:
fd.readData()
incVars = 0
_genotype = fd.genotype_1
_strains, _vals, _vars, N = fd.informativeStrains(_genotype.prgy, incVars)
self.dict['title'] = 'Pair-Scan Plot'
if not self.openMysql():
return
iPermuCheck = fd.formdata.getvalue('directPermuCheckbox')
try:
graphtype = int(fd.formdata.getvalue('graphtype'))
except:
graphtype = 1
try:
graphsort = int(fd.formdata.getvalue('graphSort'))
except:
graphsort = 1
try:
returnIntervalPairNum = int(fd.formdata.getvalue('pairScanReturn'))
except:
returnIntervalPairNum = 50
pairIntro = HT.Blockquote("The graph below displays pair-scan results for the trait ",HT.Strong(" %s" % fd.identification))
if not graphsort:
tblIntro = HT.Blockquote('This table lists LRS scores for the top %d pairs of intervals (Interval 1 on the left and Interval 2 on the right). Pairs are sorted by the "LRS Full" column. Both intervals are defined by proximal and distal markers that flank the single best position.' % returnIntervalPairNum)
else:
tblIntro = HT.Blockquote('This table lists LRS scores for the top %d pairs of intervals (Interval 1 on the left and Interval 2 on the right). Pairs are sorted by the "LRS Interaction" column. Both intervals are defined by proximal and distal markers that flank the single best position.' % returnIntervalPairNum)
try:
thisTrait = webqtlTrait(fullname=fd.formdata.getvalue("fullname"), cursor=self.cursor)
pairIntro.append(' from the database ' , thisTrait.db.genHTML())
except:
pass
pairIntro.append('. The upper left half of the plot highlights any epistatic interactions (corresponding to the column labeled "LRS Interact"). In contrast, the lower right half provides a summary of LRS of the full model, representing cumulative effects of linear and non-linear terms (column labeled "LRS Full"). The WebQTL implementation of the scan for 2-locus epistatic interactions is based on the DIRECT global optimization algorithm developed by ',HT.Href(text ="Ljungberg",url='http://user.it.uu.se/~kl/qtl_software.html',target="_blank", Class = "fs14 fwn"),', Holmgren, and Carlborg (',HT.Href(text = "2004",url='http://bioinformatics.oupjournals.org/cgi/content/abstract/bth175?ijkey=21Pp0pgOuBL6Q&keytype=ref', Class = "fs14 fwn"),').')
main_title = HT.Paragraph("Pair-Scan Results: An Analysis of Epistatic Interactions")
main_title.__setattr__("class","title")
subtitle1 = HT.Paragraph("Pair-Scan Graph")
subtitle3 = HT.Paragraph("Pair-Scan Top LRS")
subtitle1.__setattr__("class","subtitle")
subtitle3.__setattr__("class","subtitle")
self.identification = "unnamed trait"
if fd.identification:
self.identification = fd.identification
self.dict['title'] = self.identification + ' / '+self.dict['title']
#####################################
#
# Remove the Parents & F1 data
#
#####################################
if _vals:
if len(_vals) > webqtlConfig.KMININFORMATIVE:
ResultFull = []
ResultInteract = []
ResultAdd = []
#permutation test
subtitle2 = ''
permuTbl = ''
permuIntro = ''
if iPermuCheck:
subtitle2 = HT.Paragraph("Pair-Scan Permutation Results")
subtitle2.__setattr__("class","subtitle")
permuIntro = HT.Blockquote("Phenotypes were randomly permuted 500 times among strains or individuals and reanalyzed using the pair-scan algorithm. We extracted the single highest LRS for the full model for each of these permuted data sets. The histograms of these highest LRS values provide an empirical way to estimate the probability of obtaining an LRS above suggestive or significant thresholds.")
prtmuTblIntro1 = HT.Paragraph("The following table gives threshold values for Suggestive (P=0.63) and Significant associations (P=0.05) defined by Lander & Kruglyak and for the slightly more stringent P=0.01 level. (The Highly Significant level of Lander & Kruglyak corresponds to P=0.001 and cannot be estimated with 500 permutations.)")
prtmuTblIntro2 = HT.Paragraph("If the full model exceeds the permutation-based Significant threshold, then different models for those locations can be tested by conventional chi-square tests at P<0.01. Interaction is significant if LRS Interact exceeds 6.64 for RI strains or 13.28 for an F2. If interaction is not significant, the two-QTL model is better than a one-QTL model if LRS Additive exceeds LRS 1 or LRS 2 by 6.64 for RI strains or 9.21 for an F2.")
ResultFull, ResultInteract, ResultAdd = direct.permu(webqtlConfig.GENODIR, _vals, _strains, fd.RISet, 500) #XZ, 08/14/2008: add module name webqtlConfig
ResultFull.sort()
ResultInteract.sort()
ResultAdd.sort()
nPermuResult = len(ResultFull)
# draw Histogram
cFull = pid.PILCanvas(size=(400,300))
Plot.plotBar(cFull, ResultFull,XLabel='LRS',YLabel='Frequency',title=' Histogram of LRS Full')
#plotBar(cFull,10,10,390,290,ResultFull,XLabel='LRS',YLabel='Frequency',title=' Histogram of LRS Full')
filename= webqtlUtil.genRandStr("Pair_")
cFull.save(webqtlConfig.IMGDIR+filename, format='gif')
imgFull=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of LRS Full')
superPermuTbl = HT.TableLite(border=0, cellspacing=0, cellpadding=0,bgcolor ='#999999')
permuTbl2 = HT.TableLite(border=0, cellspacing= 1, cellpadding=5)
permuTbl2.append(HT.TR(HT.TD(HT.Font('LRS', color = '#FFFFFF')), HT.TD(HT.Font('p = 0.63', color = '#FFFFFF'), width = 150, align='Center'), HT.TD(HT.Font('p = 0.05', color = '#FFFFFF'), width = 150, align='Center'), HT.TD(HT.Font('p = 0.01', color = '#FFFFFF'), width = 150, align='Center'),bgColor='royalblue'))
permuTbl2.append(HT.TR(HT.TD('Full'), HT.TD('%2.1f' % ResultFull[int(nPermuResult*0.37 -1)], align="Center"), HT.TD('%2.1f' % ResultFull[int(nPermuResult*0.95 -1)], align="Center"), HT.TD('%2.1f' % ResultFull[int(nPermuResult*0.99 -1)], align="Center"),bgColor="#eeeeee"))
superPermuTbl.append(HT.TD(HT.TD(permuTbl2)))
permuTbl1 = HT.TableLite(border=0, cellspacing= 0, cellpadding=5,width='100%')
permuTbl1.append(HT.TR(HT.TD(imgFull, align="Center", width = 410), HT.TD(prtmuTblIntro1, superPermuTbl, prtmuTblIntro2, width = 490)))
permuTbl = HT.Center(permuTbl1, HT.P())
#permuTbl.append(HT.TR(HT.TD(HT.BR(), 'LRS Full = %2.1f, ' % ResultFull[int(nPermuResult*0.37 -1)], 'LRS Full = %2.1f, ' % ResultFull[int(nPermuResult*0.95 -1)], 'LRS Full highly significant (p=0.001) = %2.1f, ' % ResultFull[int(nPermuResult*0.999 -1)] , HT.BR(), 'LRS Interact suggestive (p=0.63) = %2.1f, ' % ResultInteract[int(nPermuResult*0.37 -1)], 'LRS Interact significant (p=0.05) = %2.1f, ' % ResultInteract[int(nPermuResult*0.95 -1)], 'LRS Interact = %2.1f, ' % ResultInteract[int(nPermuResult*0.999 -1)] , HT.BR(),'LRS Additive suggestive (p=0.63) = %2.1f, ' % ResultAdd[int(nPermuResult*0.37 -1)], 'LRS Additive significant (p=0.05) = %2.1f, ' % ResultAdd[int(nPermuResult*0.95 -1)], 'LRS Additive highly significant (p=0.001) = %2.1f, ' % ResultAdd[int(nPermuResult*0.999 -1)], HT.BR(), 'Total number of permutation is %d' % nPermuResult, HT.BR(), HT.BR(),colspan=2)))
#tblIntro.append(HT.P(), HT.Center(permuTbl))
#print vals, strains, fd.RISet
d = direct.direct(webqtlConfig.GENODIR, _vals, _strains, fd.RISet, 8000)#XZ, 08/14/2008: add module name webqtlConfig
chrsInfo = d[2]
sum = 0
offsets = [0]
i = 0
for item in chrsInfo:
if i > 0:
offsets.append(sum)
sum += item[0]
i += 1
offsets.append(sum)
#print sum,offset,d[2]
canvasWidth = 880
canvasHeight = 880
if graphtype:
colorAreaWidth = 230
else:
colorAreaWidth = 0
c = pid.PILCanvas(size=(canvasWidth + colorAreaWidth ,canvasHeight))
xoffset = 40
yoffset = 40
width = canvasWidth - xoffset*2
height = canvasHeight - yoffset*2
xscale = width/sum
yscale = height/sum
rectInfo = d[1]
rectInfo.sort(webqtlUtil.cmpLRSFull)
finecolors = Plot.colorSpectrum(250)
finecolors.reverse()
regLRS = [0]*height
#draw LRS Full
for item in rectInfo:
LRSFull,LRSInteract,LRSa,LRSb,chras,chram,chrae,chrbs,chrbm,chrbe,chra,chrb,flanka,flankb = item
if LRSFull > 30:
dcolor = pid.red
elif LRSFull > 20:
dcolor = pid.orange
elif LRSFull > 10:
dcolor = pid.olivedrab
elif LRSFull > 0:
dcolor = pid.grey
else:
LRSFull = 0
dcolor = pid.grey
chras += offsets[chra]
chram += offsets[chra]
chrae += offsets[chra]
chrbs += offsets[chrb]
chrbm += offsets[chrb]
chrbe += offsets[chrb]
regLRSD = int(chram*yscale)
if regLRS[regLRSD] < LRSa:
regLRS[regLRSD] = LRSa
regLRSD = int(chrbm*yscale)
if regLRS[regLRSD] < LRSb:
regLRS[regLRSD] = LRSb
if graphtype:
colorIndex = int(LRSFull *250 /LRSFullThresh)
if colorIndex >= 250:
colorIndex = 249
dcolor = finecolors[colorIndex]
if chra != chrb or ((chrbe - chrae) > 10 and (chrbs - chras) > 10):
c.drawRect(xoffset+chrbs*xscale,yoffset+height-chras*yscale,xoffset+chrbe*xscale,yoffset+height-chrae*yscale,edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0)
else:
c.drawPolygon([(xoffset+chrbs*xscale,yoffset+height-chras*yscale),(xoffset+chrbe*xscale,yoffset+height-chras*yscale),(xoffset+chrbe*xscale,yoffset+height-chrae*yscale)],edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0,closed =1)
else:
c.drawCross(xoffset+chrbm*xscale,yoffset+height-chram*yscale,color=dcolor,size=2)
#draw Marker Regression LRS
if graphtype:
"""
maxLRS = max(regLRS)
pts = []
i = 0
for item in regLRS:
pts.append((xoffset+width+35+item*50/maxLRS, yoffset+height-i))
i += 1
c.drawPolygon(pts,edgeColor=pid.blue,edgeWidth=1,closed=0)
"""
LRS1Thresh = 16.2
i = 0
for item in regLRS:
colorIndex = int(item *250 /LRS1Thresh)
if colorIndex >= 250:
colorIndex = 249
dcolor = finecolors[colorIndex]
c.drawLine(xoffset+width+35,yoffset+height-i,xoffset+width+55,yoffset+height-i,color=dcolor)
i += 1
labelFont=pid.Font(ttf="arial",size=20,bold=0)
c.drawString('Single Locus Regression',xoffset+width+90,yoffset+height, font = labelFont,color=pid.dimgray,angle=90)
#draw LRS Interact
rectInfo.sort(webqtlUtil.cmpLRSInteract)
for item in rectInfo:
LRSFull,LRSInteract,LRSa,LRSb,chras,chram,chrae,chrbs,chrbm,chrbe,chra,chrb,flanka,flankb = item
if LRSInteract > 30:
dcolor = pid.red
elif LRSInteract > 20:
dcolor = pid.orange
elif LRSInteract > 10:
dcolor = pid.olivedrab
elif LRSInteract > 0:
dcolor = pid.grey
else:
LRSInteract = 0
dcolor = pid.grey
chras += offsets[chra]
chram += offsets[chra]
chrae += offsets[chra]
chrbs += offsets[chrb]
chrbm += offsets[chrb]
chrbe += offsets[chrb]
if graphtype:
colorIndex = int(LRSInteract *250 / LRSInteractThresh )
if colorIndex >= 250:
colorIndex = 249
dcolor = finecolors[colorIndex]
if chra != chrb or ((chrbe - chrae) > 10 and (chrbs - chras) > 10):
c.drawRect(xoffset+chras*xscale,yoffset+height-chrbs*yscale,xoffset+chrae*xscale,yoffset+height-chrbe*yscale,edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0)
else:
c.drawPolygon([(xoffset+chras*xscale,yoffset+height-chrbs*yscale),(xoffset+chras*xscale,yoffset+height-chrbe*yscale),(xoffset+chrae*xscale,yoffset+height-chrbe*yscale)],edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0,closed =1)
else:
c.drawCross(xoffset+chram*xscale,yoffset+height-chrbm*yscale,color=dcolor,size=2)
#draw chromosomes label
labelFont=pid.Font(ttf="tahoma",size=24,bold=0)
i = 0
for item in chrsInfo:
strWidth = c.stringWidth(item[1],font=labelFont)
c.drawString(item[1],xoffset+offsets[i]*xscale +(item[0]*xscale-strWidth)/2,canvasHeight -15,font = labelFont,color=pid.dimgray)
c.drawString(item[1],xoffset+offsets[i]*xscale +(item[0]*xscale-strWidth)/2,yoffset-10,font = labelFont,color=pid.dimgray)
c.drawString(item[1],xoffset-strWidth-5,yoffset+height - offsets[i]*yscale -(item[0]*yscale-22)/2,font = labelFont,color=pid.dimgray)
c.drawString(item[1],canvasWidth-xoffset+5,yoffset+height - offsets[i]*yscale -(item[0]*yscale-22)/2,font = labelFont,color=pid.dimgray)
i += 1
c.drawRect(xoffset,yoffset,xoffset+width,yoffset+height)
for item in offsets:
c.drawLine(xoffset,yoffset+height-item*yscale,xoffset+width,yoffset+height-item*yscale)
c.drawLine(xoffset+item*xscale,yoffset,xoffset+item*xscale,yoffset+height)
#draw pngMap
pngMap = HT.Map(name='pairPlotMap')
#print offsets, len(offsets)
for i in range(len(offsets)-1):
for j in range(len(offsets)-1):
COORDS = "%d,%d,%d,%d" %(xoffset+offsets[i]*xscale, yoffset+height-offsets[j+1]*yscale, xoffset+offsets[i+1]*xscale, yoffset+height-offsets[j]*yscale)
HREF = "javascript:showPairPlot(%d,%d);" % (i,j)
Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
pngMap.areas.append(Areas)
#draw spectrum
if graphtype:
i = 0
labelFont=pid.Font(ttf="tahoma",size=14,bold=0)
middleoffsetX = 180
for dcolor in finecolors:
if i % 50 == 0:
c.drawLine(xoffset+ width +middleoffsetX-15 , height + yoffset -i, xoffset+ width +middleoffsetX-20,height + yoffset -i, color=pid.black)
c.drawString('%d' % int(LRSInteractThresh*i/250.0),xoffset+ width+ middleoffsetX-40,height + yoffset -i +5, font = labelFont,color=pid.black)
c.drawLine(xoffset+ width +middleoffsetX+15 , height + yoffset -i, xoffset+ width +middleoffsetX+20 ,height + yoffset -i, color=pid.black)
c.drawString('%d' % int(LRSFullThresh*i/250.0),xoffset+ width + middleoffsetX+25,height + yoffset -i +5, font = labelFont,color=pid.black)
c.drawLine(xoffset+ width +middleoffsetX-15 , height + yoffset -i, xoffset+ width +middleoffsetX+15 ,height + yoffset -i, color=dcolor)
i += 1
if i % 50 == 0:
i -= 1
c.drawLine(xoffset+ width +middleoffsetX-15 , height + yoffset -i, xoffset+ width +middleoffsetX-20,height + yoffset -i, color=pid.black)
c.drawString('%d' % ceil(LRSInteractThresh*i/250.0),xoffset+ width + middleoffsetX-40,height + yoffset -i +5, font = labelFont,color=pid.black)
c.drawLine(xoffset+ width +middleoffsetX+15 , height + yoffset -i, xoffset+ width +middleoffsetX+20 ,height + yoffset -i, color=pid.black)
c.drawString('%d' % ceil(LRSFullThresh*i/250.0),xoffset+ width + middleoffsetX+25,height + yoffset -i +5, font = labelFont,color=pid.black)
labelFont=pid.Font(ttf="verdana",size=20,bold=0)
c.drawString('LRS Interaction',xoffset+ width + middleoffsetX-50,height + yoffset, font = labelFont,color=pid.dimgray,angle=90)
c.drawString('LRS Full',xoffset+ width + middleoffsetX+50,height + yoffset, font = labelFont,color=pid.dimgray,angle=90)
filename= webqtlUtil.genRandStr("Pair_")
c.save(webqtlConfig.IMGDIR+filename, format='png')
img2=HT.Image('/image/'+filename+'.png',border=0,usemap='#pairPlotMap')
form0 = HT.Form( cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showPairPlot', submit=HT.Input(type='hidden'))
hddn0 = {'FormID':'pairPlot','Chr_A':'_','Chr_B':'','idata':string.join(map(str, _vals), ','),'istrain':string.join(_strains, ','),'RISet':fd.RISet}
for key in hddn0.keys():
form0.append(HT.Input(name=key, value=hddn0[key], type='hidden'))
form0.append(img2, pngMap)
mainfmName = webqtlUtil.genRandStr("fm_")
txtform = HT.Form( cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=mainfmName, submit=HT.Input(type='hidden'))
hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_','RISet':fd.RISet}
#XZ, Aug 11, 2010: The variable traitStrains is not assigned right values before (should not be assigned fd.strainlist).
#hddn['traitStrains'] = string.join(fd.strainlist, ',')
hddn['traitStrains'] = string.join(_strains, ',')
hddn['traitValues'] = string.join(map(str, _vals), ',')
hddn['interval1'] = ''
hddn['interval2'] = ''
if fd.incparentsf1:
hddn['incparentsf1']='ON'
for key in hddn.keys():
txtform.append(HT.Input(name=key, value=hddn[key], type='hidden'))
tbl = HT.TableLite(Class="collap", cellspacing=1, cellpadding=5,width=canvasWidth + colorAreaWidth)
c1 = HT.TD('Interval 1',colspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
c2 = HT.TD('Interval 2',colspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
c11 = HT.TD('Position',rowspan=2,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
c12 = HT.TD('Flanking Markers',colspan=2,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
c111 = HT.TD('Proximal',align="Center", Class="fs13 fwb ffl b1 cw cbrb")
c112 = HT.TD('Distal',align="Center", Class="fs13 fwb ffl b1 cw cbrb")
c3 = HT.TD('LRS Full',rowspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
c4 = HT.TD('LRS Additive',rowspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
c5 = HT.TD('LRS Interact',rowspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
c6 = HT.TD('LRS 1',rowspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
c7 = HT.TD('LRS 2',rowspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
tbl.append(HT.TR(c1,c3,c4,c5,c6,c7,c2))
tbl.append(HT.TR(c11,c12,c11,c12))
tbl.append(HT.TR(c111,c112,c111,c112))
if not graphsort: #Sort by LRS Full
rectInfo.sort(webqtlUtil.cmpLRSFull)
rectInfoReturned = rectInfo[len(rectInfo) - returnIntervalPairNum:]
rectInfoReturned.reverse()
for item in rectInfoReturned:
LRSFull,LRSInteract,LRSa,LRSb,chras,chram,chrae,chrbs,chrbm,chrbe,chra,chrb,flanka,flankb = item
LRSAdditive = LRSFull - LRSInteract
flanka1,flanka2 = string.split(flanka)
flankb1,flankb2 = string.split(flankb)
urla1 = HT.Href(text = flanka1, url = "javascript:showTrait('%s','%s');" % (mainfmName, flanka1),Class= "fs12 fwn")
urla2 = HT.Href(text = flanka2, url = "javascript:showTrait('%s','%s');" % (mainfmName, flanka2),Class= "fs12 fwn")
urlb1 = HT.Href(text = flankb1, url = "javascript:showTrait('%s','%s');" % (mainfmName, flankb1),Class= "fs12 fwn")
urlb2 = HT.Href(text = flankb2, url = "javascript:showTrait('%s','%s');" % (mainfmName, flankb2),Class= "fs12 fwn")
urlGenGraph = HT.Href(text = "Plot", url = "javascript:showCateGraph('%s', '%s %s %2.3f', '%s %s %2.3f');" % (mainfmName, flanka1, flanka2, chram, flankb1, flankb2, chrbm),Class= "fs12 fwn")
tr1 = HT.TR(
HT.TD('Chr %s @ %2.1f cM ' % (chrsInfo[chra][1],chram),Class= "fs12 b1 fwn"),
HT.TD(urla1,Class= "fs12 b1 fwn"),
HT.TD(urla2,Class= "fs12 b1 fwn"),
HT.TD('%2.3f ' % LRSFull, urlGenGraph,Class= "fs12 b1 fwn"),
HT.TD('%2.3f' % LRSAdditive,Class= "fs12 b1 fwn"),
HT.TD('%2.3f' % LRSInteract,Class= "fs12 b1 fwn"),
HT.TD('%2.3f' % LRSa,Class= "fs12 b1 fwn"),
HT.TD('%2.3f' % LRSb,Class= "fs12 b1 fwn"),
HT.TD('Chr %s @ %2.1f cM' % (chrsInfo[chrb][1],chrbm),Class= "fs12 b1 fwn"),
HT.TD(urlb1,Class= "fs12 b1 fwn"),
HT.TD(urlb2,Class= "fs12 b1 fwn"))
tbl.append(tr1)
plotType1 = HT.Input(type="radio", name="plotType", value ="Dot", checked=1)
plotType2 = HT.Input(type="radio", name="plotType", value ="Box")
plotText = HT.Paragraph("Plot Type : ", plotType1, " Dot ", plotType2, " Box", )
txtform.append(plotText, tbl)
TD_LR = HT.TD(colspan=2,height=200,width="100%",bgColor='#eeeeee')
TD_LR.append(main_title,HT.Blockquote(subtitle1, pairIntro, HT.P(), HT.Center(form0,HT.P())),HT.Blockquote(subtitle2, permuIntro,HT.P(), HT.Center(permuTbl)), HT.Blockquote(subtitle3, tblIntro, HT.P(),HT.Center(txtform), HT.P()))
self.dict['body'] = str(TD_LR)
else:
heading = "Direct Plot"
detail = ['Fewer than %d strain data were entered for %s data set. No statitical analysis has been attempted.' % (webqtlConfig.KMININFORMATIVE, fd.RISet)]
self.error(heading=heading,detail=detail)
return
else:
heading = "Direct Plot"
detail = ['Empty data set, please check your data.']
self.error(heading=heading,detail=detail)
return
def __init__(self,fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
if not fd.genotype:
fd.readGenotype()
self.searchResult = fd.formdata.getvalue('searchResult')
if not self.searchResult:
templatePage.__init__(self, fd)
heading = 'QTL Heatmap'
detail = ['You need to select at least two traits in order to generate correlation matrix.']
self.error(heading=heading,detail=detail)
return
if type("1") == type(self.searchResult):
self.searchResult = string.split(self.searchResult,'\t')
if self.searchResult:
if len(self.searchResult) > webqtlConfig.MAXCORR:
heading = 'QTL Heatmap'
detail = ['In order to display the QTL heat map properly, do not select more than %d traits for analysis.' % webqtlConfig.MAXCORR]
self.error(heading=heading,detail=detail)
return
traitList = []
traitDataList = []
for item in self.searchResult:
thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
thisTrait.retrieveInfo()
thisTrait.retrieveData(fd.strainlist)
traitList.append(thisTrait)
traitDataList.append(thisTrait.exportData(fd.strainlist))
else:
heading = 'QTL Heatmap'
detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')]
self.error(heading=heading,detail=detail)
return
self.colorScheme = fd.formdata.getvalue('colorScheme')
if not self.colorScheme:
self.colorScheme = '1'
self.dict['title'] = 'QTL heatmap'
NNN = len(traitList)
if NNN == 0:
heading = "QTL Heatmap"
detail = ['No trait was selected for %s data set. No QTL heatmap was generated.' % fd.RISet]
self.error(heading=heading,detail=detail)
return
elif NNN < 2:
templatePage.__init__(self, fd)
heading = 'QTL Heatmap'
detail = ['You need to select at least two traits in order to generate QTL heatmap.']
self.error(heading=heading,detail=detail)
return
else:
#XZ: It's necessory to define canvas here
canvas = pid.PILCanvas(size=(80+NNN*20,880))
names = map(webqtlTrait.displayName, traitList)
self.targetDescriptionChecked = fd.formdata.getvalue('targetDescriptionCheck', '')
#XZ, 7/29/2009: create trait display and find max strWidth
strWidth = 0
for j in range(len(names)):
thisTrait = traitList[j]
if self.targetDescriptionChecked:
if thisTrait.db.type == 'ProbeSet':
if thisTrait.probe_target_description:
names[j] += ' [%s at Chr %s @ %2.3fMB, %s]' % (thisTrait.symbol, thisTrait.chr, thisTrait.mb, thisTrait.probe_target_description)
else:
names[j] += ' [%s at Chr %s @ %2.3fMB]' % (thisTrait.symbol, thisTrait.chr, thisTrait.mb)
elif thisTrait.db.type == 'Geno':
names[j] += ' [Chr %s @ %2.3fMB]' % (thisTrait.chr, thisTrait.mb)
elif thisTrait.db.type == 'Publish':
if thisTrait.abbreviation:
names[j] += ' [%s]' % (thisTrait.abbreviation)
else:
pass
else:
pass
i = canvas.stringWidth(names[j],font=self.labelFont)
if i > strWidth:
strWidth = i
width = NNN*20
xoffset = 40
yoffset = 40
cellHeight = 3
nLoci = reduce(lambda x,y: x+y, map(lambda x: len(x),fd.genotype),0)
if nLoci > 2000:
cellHeight = 1
elif nLoci > 1000:
cellHeight = 2
elif nLoci < 200:
cellHeight = 10
else:
pass
pos = range(NNN)
neworder = []
BWs = Plot.BWSpectrum()
colors100 = Plot.colorSpectrum()
colors = Plot.colorSpectrum(130)
finecolors = Plot.colorSpectrum(250)
colors100.reverse()
colors.reverse()
finecolors.reverse()
scaleFont=pid.Font(ttf="tahoma",size=10,bold=0)
self.clusterChecked = fd.formdata.getvalue('clusterCheck', '')
if not self.clusterChecked: #XZ: this part is for original order
for i in range(len(names)):
neworder.append((xoffset+20*(i+1), i))
canvas = pid.PILCanvas(size=(80+NNN*20+240,80+ self.topHeight +5+5+strWidth+nLoci*cellHeight+80+20*cellHeight))
self.drawTraitNameBottom(canvas,names,yoffset,neworder,strWidth)
else: #XZ: this part is to cluster traits
self.topHeight = 400
canvas = pid.PILCanvas(size=(80+NNN*20+240,80+ self.topHeight +5+5+strWidth+nLoci*cellHeight+80+20*cellHeight))
corArray = [([0] * (NNN))[:] for i in range(NNN)]
nnCorr = len(fd.strainlist)
#XZ, 08/04/2009: I commented out pearsonArray, spearmanArray
for i, thisTrait in enumerate(traitList):
names1 = [thisTrait.db.name, thisTrait.name, thisTrait.cellid]
for j, thisTrait2 in enumerate(traitList):
names2 = [thisTrait2.db.name, thisTrait2.name, thisTrait2.cellid]
if j < i:
corr,nOverlap = webqtlUtil.calCorrelation(traitDataList[i],traitDataList[j],nnCorr)
if (1-corr) < 0:
distance = 0.0
else:
distance = 1-corr
corArray[i][j] = distance
corArray[j][i] = distance
elif j == i:
corArray[i][j] = 0.0
else:
pass
#XZ, 7/29/2009: The parameter d has info of cluster (group member and distance). The format of d is tricky. Print it out to see it's format.
d = slink.slink(corArray)
#XZ, 7/29/2009: Attention: The 'neworder' is changed by the 'draw' function
#XZ, 7/30/2009: Only toppos[1][0] and top[1][1] are used later. Then what toppos[0] is used for?
toppos = self.draw(canvas,names,d,xoffset,yoffset,neworder)
self.drawTraitNameTop(canvas,names,yoffset,neworder,strWidth)
#XZ, 7/29/2009: draw the top vertical line
canvas.drawLine(toppos[1][0],toppos[1][1],toppos[1][0],yoffset)
#XZ: draw string 'distance = 1-r'
canvas.drawString('distance = 1-r',neworder[-1][0] + 50, self.topHeight*3/4,font=self.labelFont,angle=90)
#draw Scale
scaleFont=pid.Font(ttf="tahoma",size=10,bold=0)
x = neworder[-1][0]
canvas.drawLine(x+5, self.topHeight+yoffset, x+5, yoffset, color=pid.black)
y = 0
while y <=2:
canvas.drawLine(x+5, self.topHeight*y/2.0+yoffset, x+10, self.topHeight*y/2.0+yoffset)
canvas.drawString('%2.1f' % (2-y), x+12, self.topHeight*y/2.0+yoffset, font=scaleFont)
y += 0.5
chrname = 0
chrnameFont=pid.Font(ttf="tahoma",size=24,bold=0)
Ncol = 0
gifmap = HT.Map(name='traitMap')
nearestMarkers = self.getNearestMarker(traitList, fd.genotype)
# import cPickle
sessionfile = fd.formdata.getvalue("session")
if sessionfile:
fp = open(os.path.join(webqtlConfig.TMPDIR, sessionfile + '.session'), 'rb')
permData = cPickle.load(fp)
fp.close()
else:
permData = {}
#XZ, 7/31/2009: This for loop is to generate the heatmap
#XZ: draw trait by trait instead of marker by marker
for order in neworder:
#startHeight = 40+400+5+5+strWidth
startHeight = self.topHeight + 40+5+5+strWidth
startWidth = order[0]-5
if Ncol and Ncol % 5 == 0:
drawStartPixel = 8
else:
drawStartPixel = 9
tempVal = traitDataList[order[1]]
_vals = []
_strains = []
for i in range(len(fd.strainlist)):
if tempVal[i] != None:
_strains.append(fd.strainlist[i])
_vals.append(tempVal[i])
qtlresult = fd.genotype.regression(strains = _strains, trait = _vals)
if sessionfile:
LRSArray = permData[str(traitList[order[1]])]
else:
LRSArray = fd.genotype.permutation(strains = _strains, trait = _vals, nperm = 1000)
permData[str(traitList[order[1]])] = LRSArray
sugLRS = LRSArray[369]
sigLRS = LRSArray[949]
prechr = 0
chrstart = 0
nearest = nearestMarkers[order[1]]
midpoint = []
for item in qtlresult:
if item.lrs > webqtlConfig.MAXLRS:
adjustlrs = webqtlConfig.MAXLRS
else:
adjustlrs = item.lrs
if item.locus.chr != prechr:
if prechr:
canvas.drawRect(startWidth-drawStartPixel, startHeight, startWidth+10, startHeight+3,edgeColor=pid.white, edgeWidth=0, fillColor=pid.white)
startHeight+= 3
if not chrname:
canvas.drawString(prechr,xoffset-20,(chrstart+startHeight)/2,font = chrnameFont,color=pid.dimgray)
prechr = item.locus.chr
chrstart = startHeight
if self.colorScheme == '0':
if adjustlrs <= sugLRS:
colorIndex = int(65*adjustlrs/sugLRS)
else:
colorIndex = int(65 + 35*(adjustlrs-sugLRS)/(sigLRS-sugLRS))
if colorIndex > 99:
colorIndex = 99
colorIndex = colors100[colorIndex]
elif self.colorScheme == '1':
sugLRS = LRSArray[369]/2.0
if adjustlrs <= sugLRS:
colorIndex = BWs[20+int(50*adjustlrs/sugLRS)]
else:
if item.additive > 0:
colorIndex = int(80 + 50*(adjustlrs-sugLRS)/(sigLRS-sugLRS))
else:
colorIndex = int(50 - 50*(adjustlrs-sugLRS)/(sigLRS-sugLRS))
if colorIndex > 129:
colorIndex = 129
if colorIndex < 0:
colorIndex = 0
colorIndex = colors[colorIndex]
elif self.colorScheme == '2':
if item.additive > 0:
colorIndex = int(150 + 100*(adjustlrs/sigLRS))
else:
colorIndex = int(100 - 100*(adjustlrs/sigLRS))
if colorIndex > 249:
colorIndex = 249
if colorIndex < 0:
colorIndex = 0
colorIndex = finecolors[colorIndex]
else:
colorIndex = pid.white
if startHeight > 1:
canvas.drawRect(startWidth-drawStartPixel, startHeight, startWidth+10, startHeight+cellHeight,edgeColor=colorIndex, edgeWidth=0, fillColor=colorIndex)
else:
canvas.drawLine(startWidth-drawStartPixel, startHeight, startWidth+10, startHeight, Color=colorIndex)
if item.locus.name == nearest:
midpoint = [startWidth,startHeight-5]
startHeight+=cellHeight
#XZ, map link to trait name and band
COORDS = "%d,%d,%d,%d" %(startWidth-drawStartPixel,self.topHeight+40,startWidth+10,startHeight)
HREF = "javascript:showDatabase2('%s','%s','%s');" % (traitList[order[1]].db.name, traitList[order[1]].name, traitList[order[1]].cellid)
Areas = HT.Area(shape='rect',coords=COORDS,href=HREF, title='%s' % names[order[1]])
gifmap.areas.append(Areas)
if midpoint:
traitPixel = ((midpoint[0],midpoint[1]),(midpoint[0]-6,midpoint[1]+12),(midpoint[0]+6,midpoint[1]+12))
canvas.drawPolygon(traitPixel,edgeColor=pid.black,fillColor=pid.orange,closed=1)
if not chrname:
canvas.drawString(prechr,xoffset-20,(chrstart+startHeight)/2,font = chrnameFont,color=pid.dimgray)
chrname = 1
Ncol += 1
#draw Spectrum
startSpect = neworder[-1][0] + 30
startHeight = self.topHeight + 40+5+5+strWidth
if self.colorScheme == '0':
for i in range(100):
canvas.drawLine(startSpect+i,startHeight+20,startSpect+i,startHeight+40,color=colors100[i])
scaleFont=pid.Font(ttf="tahoma",size=10,bold=0)
canvas.drawLine(startSpect,startHeight+45,startSpect,startHeight+39,color=pid.black)
canvas.drawString('LRS = 0',startSpect,startHeight+55,font=scaleFont)
canvas.drawLine(startSpect+64,startHeight+45,startSpect+64,startHeight+39,color=pid.black)
canvas.drawString('Suggestive LRS',startSpect+64,startHeight+55,font=scaleFont)
canvas.drawLine(startSpect+99,startHeight+45,startSpect+99,startHeight+39,color=pid.black)
canvas.drawString('Significant LRS',startSpect+105,startHeight+40,font=scaleFont)
elif self.colorScheme == '1':
for i in range(50):
canvas.drawLine(startSpect+i,startHeight,startSpect+i,startHeight+40,color=BWs[20+i])
for i in range(50,100):
canvas.drawLine(startSpect+i,startHeight,startSpect+i,startHeight+20,color=colors[100-i])
canvas.drawLine(startSpect+i,startHeight+20,startSpect+i,startHeight+40,color=colors[30+i])
canvas.drawLine(startSpect,startHeight+45,startSpect,startHeight+39,color=pid.black)
canvas.drawString('LRS = 0',startSpect,startHeight+60,font=scaleFont)
canvas.drawLine(startSpect+50,startHeight+45,startSpect+50,startHeight+39,color=pid.black)
canvas.drawString('0.5*Suggestive LRS',startSpect+50,startHeight+ 60,font=scaleFont)
canvas.drawLine(startSpect+99,startHeight+45,startSpect+99,startHeight+39,color=pid.black)
canvas.drawString('Significant LRS',startSpect+105,startHeight+50,font=scaleFont)
textFont=pid.Font(ttf="verdana",size=18,bold=0)
canvas.drawString('%s +' % fd.ppolar,startSpect+120,startHeight+ 35,font=textFont,color=pid.red)
canvas.drawString('%s +' % fd.mpolar,startSpect+120,startHeight+ 15,font=textFont,color=pid.blue)
elif self.colorScheme == '2':
for i in range(100):
canvas.drawLine(startSpect+i,startHeight,startSpect+i,startHeight+20,color=finecolors[100-i])
canvas.drawLine(startSpect+i,startHeight+20,startSpect+i,startHeight+40,color=finecolors[150+i])
canvas.drawLine(startSpect,startHeight+45,startSpect,startHeight+39,color=pid.black)
canvas.drawString('LRS = 0',startSpect,startHeight+60,font=scaleFont)
canvas.drawLine(startSpect+99,startHeight+45,startSpect+99,startHeight+39,color=pid.black)
canvas.drawString('Significant LRS',startSpect+105,startHeight+50,font=scaleFont)
textFont=pid.Font(ttf="verdana",size=18,bold=0)
canvas.drawString('%s +' % fd.ppolar,startSpect+120,startHeight+ 35,font=textFont,color=pid.red)
canvas.drawString('%s +' % fd.mpolar,startSpect+120,startHeight+ 15,font=textFont,color=pid.blue)
filename= webqtlUtil.genRandStr("Heatmap_")
canvas.save(webqtlConfig.IMGDIR+filename, format='png')
img2=HT.Image('/image/'+filename+'.png',border=0,usemap='#traitMap')
imgUrl = 'Right-click or control-click on the link to download this graph as a <a href="/image/%s.png" class="normalsize" target="_blank">PNG file</a>' % filename
form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_','RISet':fd.RISet,'searchResult':string.join(self.searchResult,'\t')}
if fd.incparentsf1:
hddn['incparentsf1']='ON'
for key in hddn.keys():
form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
heatmap = HT.Input(type='button' ,name='mintmap',value='Redraw QTL Heatmap', onClick="databaseFunc(this.form,'heatmap');",Class="button")
spects = {'0':'Single Spectrum','1':'Grey + Blue + Red','2':'Blue + Red'}
schemeMenu = HT.Select(name='colorScheme')
schemeMenu.append(('Single Spectrum',0))
schemeMenu.append(('Grey + Blue + Red',1))
schemeMenu.append(('Blue + Red',2))
schemeMenu.selected.append(spects[self.colorScheme])
clusterCheck= HT.Input(type='checkbox', Class='checkbox', name='clusterCheck',checked=0)
targetDescriptionCheck = HT.Input(type='checkbox', Class='checkbox', name='targetDescriptionCheck',checked=0)
form.append(gifmap,schemeMenu, heatmap, HT.P(), clusterCheck, ' Cluster traits ', targetDescriptionCheck, ' Add description', HT.P(),img2, HT.P(), imgUrl)
if not sessionfile:
filename = webqtlUtil.generate_session()
webqtlUtil.dump_session(permData, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
sessionfile=filename
form.append(HT.Input(name='session', value=sessionfile, type='hidden'))
heatmapHelp = HT.Input(type='button' ,name='heatmapHelpButton',value='Info', onClick="openNewWin('/heatmap.html');",Class="button")
heatmapHeading = HT.Paragraph('QTL Heatmap ', heatmapHelp, Class="title")
TD_LR = HT.TD(colspan=2,height=200,width="100%",bgColor='#eeeeee')
TD_LR.append(heatmapHeading, HT.P(),HT.P(),HT.P(),HT.P(),HT.P(),form)
self.dict['body'] = str(TD_LR)
def __init__(self, fd):
LRSFullThresh = 30
LRSInteractThresh = 25
maxPlotSize = 1000
mainfmName = webqtlUtil.genRandStr("fm_")
templatePage.__init__(self, fd)
self.dict['title'] = 'Pair-Scan Plot'
if not self.openMysql():
return
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
vals = fd.formdata.getvalue('idata')
vals = map(float,string.split(vals,','))
strains = fd.formdata.getvalue('istrain')
strains = string.split(strains,',')
Chr_A = int(fd.formdata.getvalue('Chr_A'))
Chr_B = int(fd.formdata.getvalue('Chr_B'))
if len(vals) > webqtlConfig.KMININFORMATIVE:
d = direct.exhaust(webqtlConfig.GENODIR, vals, strains, fd.RISet, Chr_A, Chr_B)#XZ, 08/14/2008: add module name webqtlConfig
chrsInfo = d[2]
longerChrLen = max(chrsInfo[Chr_A][0], chrsInfo[Chr_B][0])
shorterChrlen = min(chrsInfo[Chr_A][0], chrsInfo[Chr_B][0])
plotHeight = int(chrsInfo[Chr_B][0]*maxPlotSize/longerChrLen)
plotWidth = int(chrsInfo[Chr_A][0]*maxPlotSize/longerChrLen)
xLeftOffset = 200
xRightOffset = 40
yTopOffset = 40
yBottomOffset = 200
colorAreaWidth = 120
canvasHeight = plotHeight + yTopOffset + yBottomOffset
canvasWidth = plotWidth + xLeftOffset + xRightOffset + colorAreaWidth
canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight))
plotScale = plotHeight/chrsInfo[Chr_B][0]
rectInfo = d[1]
finecolors = Plot.colorSpectrum(250)
finecolors.reverse()
#draw LRS Full
for item in rectInfo:
LRSFull,LRSInteract,LRSa,LRSb,chras,chram,chrae,chrbs,chrbm,chrbe,chra,chrb,flanka,flankb = item
if Chr_A > Chr_B:
colorIndex = int(LRSFull *250 /LRSFullThresh)
else:
colorIndex = int(LRSInteract *250 /LRSInteractThresh)
if colorIndex >= 250:
colorIndex = 249
elif colorIndex < 0:
colorIndex = 0
dcolor = finecolors[colorIndex]
if chra != chrb or (abs(chrbe - chrae) > 10 and abs(chrbs - chras) > 10):
canvas.drawRect(xLeftOffset+chras*plotScale,yTopOffset+plotHeight- \
chrbs*plotScale,xLeftOffset+chrae*plotScale,yTopOffset+plotHeight- \
chrbe*plotScale,edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0)
elif chrbs >= chras:
canvas.drawPolygon([(xLeftOffset+chras*plotScale,yTopOffset+plotHeight-chrbs*plotScale),\
(xLeftOffset+chras*plotScale,yTopOffset+plotHeight-chrbe*plotScale),\
(xLeftOffset+chrae*plotScale,yTopOffset+plotHeight-chrbe*plotScale)],\
edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0,closed =1)
else:
canvas.drawPolygon([(xLeftOffset+chras*plotScale,yTopOffset+plotHeight-chrbs*plotScale),\
(xLeftOffset+chrae*plotScale,yTopOffset+plotHeight-chrbs*plotScale), \
(xLeftOffset+chrae*plotScale,yTopOffset+plotHeight-chrbe*plotScale)], \
edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0,closed =1)
labelFont=pid.Font(ttf="verdana",size=24,bold=0)
chrName = "chromosome %s" % chrsInfo[Chr_A][1]
canvas.drawString(chrName,xLeftOffset + (plotWidth - canvas.stringWidth(chrName,font=labelFont))/2,\
yTopOffset+plotHeight+ 170,font=labelFont)
chrName = "chromosome %s" % chrsInfo[Chr_B][1]
canvas.drawString(chrName, 30, yTopOffset +(canvas.stringWidth(chrName,font=labelFont) + plotHeight)/2,\
font=labelFont, angle = 90)
if Chr_A == Chr_B:
infoStr = "minimum distance = 10 cM"
infoStrWidth = canvas.stringWidth(infoStr,font=labelFont)
canvas.drawString(infoStr, xLeftOffset + (plotWidth-infoStrWidth*0.707)/2, yTopOffset + \
(plotHeight+infoStrWidth*0.707)/2,font=labelFont, angle = 45, color=pid.red)
labelFont=pid.Font(ttf="verdana",size=12,bold=0)
gifmap = HT.Map(name='markerMap')
lineColor = pid.lightblue
#draw ChrA Loci
ChrAInfo = d[3]
preLpos = -1
i = 0
for item in ChrAInfo:
Lname,Lpos = item
if Lpos != preLpos:
i += 1
preLpos = Lpos
stepA = float(plotWidth)/i
offsetA = -stepA
LRectWidth = 10
LRectHeight = 3
i = 0
preLpos = -1
for item in ChrAInfo:
Lname,Lpos = item
if Lpos != preLpos:
offsetA += stepA
differ = 1
else:
differ = 0
preLpos = Lpos
Lpos *= plotScale
Zorder = i % 5
"""
LStrWidth = canvas.stringWidth(Lname,font=labelFont)
canvas.drawString(Lname,xLeftOffset+offsetA+4,yTopOffset+plotHeight+140,\
font=labelFont,color=pid.blue,angle=90)
canvas.drawLine(xLeftOffset+Lpos,yTopOffset+plotHeight,xLeftOffset+offsetA,\
yTopOffset+plotHeight+25,color=lineColor)
canvas.drawLine(xLeftOffset+offsetA,yTopOffset+plotHeight+25,xLeftOffset+offsetA,\
yTopOffset+plotHeight+140-LStrWidth,color=lineColor)
COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA+4,yTopOffset+plotHeight+140,\
xLeftOffset+offsetA-6,yTopOffset+plotHeight+140-LStrWidth)
"""
if differ:
canvas.drawLine(xLeftOffset+Lpos,yTopOffset+plotHeight,xLeftOffset+offsetA,\
yTopOffset+plotHeight+25,color=lineColor)
canvas.drawLine(xLeftOffset+offsetA,yTopOffset+plotHeight+25,xLeftOffset+offsetA,\
yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),color=lineColor)
rectColor = pid.orange
else:
canvas.drawLine(xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3)-3,\
xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),color=lineColor)
rectColor = pid.deeppink
canvas.drawRect(xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),\
xLeftOffset+offsetA-LRectHeight,yTopOffset+plotHeight+80+Zorder*(LRectWidth+3)+LRectWidth,\
edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),\
xLeftOffset+offsetA-LRectHeight,yTopOffset+plotHeight+80+Zorder*(LRectWidth+3)+LRectWidth)
HREF="javascript:showTrait('%s','%s');" % (mainfmName, Lname)
Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
gifmap.areas.append(Areas)
i += 1
#print (i , offsetA, Lname, Lpos, preLpos)
#print "<BR>"
#draw ChrB Loci
ChrBInfo = d[4]
preLpos = -1
i = 0
for item in ChrBInfo:
Lname,Lpos = item
if Lpos != preLpos:
i += 1
preLpos = Lpos
stepB = float(plotHeight)/i
offsetB = -stepB
LRectWidth = 10
LRectHeight = 3
i = 0
preLpos = -1
for item in ChrBInfo:
Lname,Lpos = item
if Lpos != preLpos:
offsetB += stepB
differ = 1
else:
differ = 0
preLpos = Lpos
Lpos *= plotScale
Zorder = i % 5
Lname,Lpos = item
Lpos *= plotScale
"""
LStrWidth = canvas.stringWidth(Lname,font=labelFont)
canvas.drawString(Lname, 45,yTopOffset+plotHeight-offsetB+4,font=labelFont,color=pid.blue)
canvas.drawLine(45+LStrWidth,yTopOffset+plotHeight-offsetB,xLeftOffset-25,\
yTopOffset+plotHeight-offsetB,color=lineColor)
canvas.drawLine(xLeftOffset-25,yTopOffset+plotHeight-offsetB,xLeftOffset,\
yTopOffset+plotHeight-Lpos,color=lineColor)
COORDS = "%d,%d,%d,%d" %(45,yTopOffset+plotHeight-offsetB+4,45+LStrWidth,\
yTopOffset+plotHeight-offsetB-6)
"""
if differ:
canvas.drawLine(xLeftOffset,yTopOffset+plotHeight-Lpos, xLeftOffset-25,\
yTopOffset+plotHeight-offsetB,color=lineColor)
canvas.drawLine(xLeftOffset -25, yTopOffset+plotHeight-offsetB, \
xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB, color=lineColor)
rectColor = pid.orange
else:
canvas.drawLine(xLeftOffset -80 -Zorder*(LRectWidth+3)+3, yTopOffset+plotHeight-offsetB, \
xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB, color=lineColor)
rectColor = pid.deeppink
HREF = "javascript:showTrait('%s','%s');" % (mainfmName, Lname)
canvas.drawRect(xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB,\
xLeftOffset-80 -Zorder*(LRectWidth+3)-LRectWidth,yTopOffset+plotHeight-offsetB +LRectHeight,\
edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
COORDS="%d,%d,%d,%d"%(xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB,\
xLeftOffset-80 -Zorder*(LRectWidth+3)-LRectWidth,yTopOffset+plotHeight-offsetB +LRectHeight)
Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
gifmap.areas.append(Areas)
i += 1
canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight,edgeColor=pid.black)
#draw spectrum
i = 0
labelFont=pid.Font(ttf="tahoma",size=14,bold=0)
middleoffsetX = 80
for dcolor in finecolors:
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX-15 , plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX+15 , plotHeight + yTopOffset - i, color=dcolor)
if i % 50 == 0:
if Chr_A >= Chr_B:
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
canvas.drawString('%d' % int(LRSFullThresh*i/250.0),xLeftOffset+ plotWidth +middleoffsetX+22,\
plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
if Chr_A <= Chr_B:
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX-15 ,plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX-20,plotHeight + yTopOffset - i, color=pid.black)
canvas.drawString('%d' % int(LRSInteractThresh*i/250.0),xLeftOffset+plotWidth+middleoffsetX-40,\
plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
i += 1
#draw spectrum label
labelFont2=pid.Font(ttf="verdana",size=20,bold=0)
if i % 50 == 0:
i -= 1
if Chr_A >= Chr_B:
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
canvas.drawString('%d' % int(LRSFullThresh*(i+1)/250.0),xLeftOffset+ plotWidth +middleoffsetX+22,\
plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
canvas.drawString('LRS Full',xLeftOffset+ plotWidth +middleoffsetX+50,plotHeight + yTopOffset, \
font = labelFont2,color=pid.dimgray,angle=90)
if Chr_A <= Chr_B:
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX-15 ,plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX-20,plotHeight + yTopOffset - i, color=pid.black)
canvas.drawString('%d' % int(LRSInteractThresh*(i+1)/250.0),xLeftOffset+ plotWidth+middleoffsetX-40,\
plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
canvas.drawString('LRS Interaction',xLeftOffset+ plotWidth +middleoffsetX-50,\
plotHeight + yTopOffset, font = labelFont2,color=pid.dimgray,angle=90)
filename= webqtlUtil.genRandStr("Pair_")
canvas.save(webqtlConfig.IMGDIR+filename, format='png')
img2=HT.Image('/image/'+filename+'.png',border=0,usemap='#markerMap')
main_title = HT.Paragraph("Pair-Scan Results: Chromosome Pair")
main_title.__setattr__("class","title")
form = HT.Form(cgi = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', \
name=mainfmName, submit=HT.Input(type='hidden'))
hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_','RISet':fd.RISet, 'incparentsf1':'on'}
if fd.incparentsf1:
hddn['incparentsf1']='ON'
for key in hddn.keys():
form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
form.append(img2,gifmap)
TD_LR.append(main_title, HT.Center(form), HT.P())
else:
heading = "Direct Plot"
detail = ['Fewer than %d strain data were entered for %s data set. No statitical analysis has been attempted.'\
% (webqtlConfig.KMININFORMATIVE, fd.RISet)]
self.error(heading=heading,detail=detail)
return
self.dict['body'] = str(TD_LR)
