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Diffstat (limited to 'web/webqtl/pairScan/PairPlotPage.py')
| -rwxr-xr-x | web/webqtl/pairScan/PairPlotPage.py | 314 |
1 files changed, 314 insertions, 0 deletions
diff --git a/web/webqtl/pairScan/PairPlotPage.py b/web/webqtl/pairScan/PairPlotPage.py new file mode 100755 index 00000000..3f72bd74 --- /dev/null +++ b/web/webqtl/pairScan/PairPlotPage.py @@ -0,0 +1,314 @@ +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See the GNU Affero General Public License for more details. +# +# This program is available from Source Forge: at GeneNetwork Project +# (sourceforge.net/projects/genenetwork/). +# +# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) +# at rwilliams@uthsc.edu and xzhou15@uthsc.edu +# +# +# +# This module is used by GeneNetwork project (www.genenetwork.org) +# +# Created by GeneNetwork Core Team 2010/08/10 +# +# Last updated by GeneNetwork Core Team 2010/10/20 + +import string +import piddle as pid +import os + +from htmlgen import HTMLgen2 as HT +import direct + +from utility import Plot +from base.templatePage import templatePage +from utility import webqtlUtil +from base import webqtlConfig + +######################################### +# PairPlotPage +######################################### +class PairPlotPage(templatePage): + 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) + + |