aboutsummaryrefslogtreecommitdiff
path: root/web/webqtl/pairScan/PairPlotPage.py
diff options
context:
space:
mode:
Diffstat (limited to 'web/webqtl/pairScan/PairPlotPage.py')
-rwxr-xr-xweb/webqtl/pairScan/PairPlotPage.py314
1 files changed, 0 insertions, 314 deletions
diff --git a/web/webqtl/pairScan/PairPlotPage.py b/web/webqtl/pairScan/PairPlotPage.py
deleted file mode 100755
index 3f72bd74..00000000
--- a/web/webqtl/pairScan/PairPlotPage.py
+++ /dev/null
@@ -1,314 +0,0 @@
-# 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)
-
-
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-21 08:39:38 +0000