# 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)