Add all the source codes into the github.

1 files changed, 199 insertions, 0 deletions

diff --git a/web/webqtl/pairScan/CategoryGraphPage.py b/web/webqtl/pairScan/CategoryGraphPage.py
new file mode 100755
index 00000000..696c05ce
--- /dev/null
+++ b/web/webqtl/pairScan/CategoryGraphPage.py
@@ -0,0 +1,199 @@
+# 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
+from htmlgen import HTMLgen2 as HT
+
+from utility import Plot
+from base.templatePage import templatePage
+from utility import webqtlUtil
+from base import webqtlConfig
+
+#########################################
+#      Category Graph Page
+#########################################
+class CategoryGraphPage(templatePage):
+	def __init__(self, fd):
+
+		LRSFullThresh = 30
+		LRSInteractThresh = 25
+		maxPlotSize = 800
+		mainfmName = webqtlUtil.genRandStr("fm_")
+
+		templatePage.__init__(self, fd)
+
+		if not fd.genotype:
+			fd.readData()
+
+		##Remove F1 and Parents
+		fd.genotype = fd.genotype_1
+
+		plotType = fd.formdata.getvalue('plotType')
+		self.dict['title'] = '%s Plot' % plotType
+		main_title = HT.Paragraph("%s Plot" % plotType)
+		main_title.__setattr__("class","title")
+
+		interval1 = fd.formdata.getvalue('interval1')
+		interval2 = fd.formdata.getvalue('interval2')
+
+		flanka1, flanka2, chram = string.split(interval1)
+		flankb1, flankb2, chrbm = string.split(interval2)
+
+		traitValues = string.split(fd.formdata.getvalue('traitValues'), ',')
+		traitValues = map(webqtlUtil.StringAsFloat, traitValues)
+		traitStrains = string.split(fd.formdata.getvalue('traitStrains'), ',')
+
+		flankaGeno = []
+		flankbGeno = []
+
+		for chr in fd.genotype:
+			for locus in chr:
+				if locus.name in (flanka1, flankb1):
+					if locus.name == flanka1:
+						flankaGeno = locus.genotype[:]
+					else:
+						flankbGeno = locus.genotype[:]
+			if flankaGeno and flankbGeno:
+				break
+
+		flankaDict = {}
+		flankbDict = {}
+		for i in range(len(fd.genotype.prgy)):
+			flankaDict[fd.genotype.prgy[i]] = flankaGeno[i]
+			flankbDict[fd.genotype.prgy[i]] = flankbGeno[i]
+
+		BB = []
+		BD = []
+		DB = []
+		DD = []
+
+		iValues = []
+		for i in range(len(traitValues)):
+			if traitValues[i] != None:
+				iValues.append(traitValues[i])
+				thisstrain = traitStrains[i]
+				try:
+					a1 = flankaDict[thisstrain]
+					b1 = flankbDict[thisstrain]
+				except:
+					continue
+				if a1 == -1.0:
+					if b1 == -1.0:
+						BB.append((thisstrain, traitValues[i]))
+					elif b1 == 1.0:
+						BD.append((thisstrain, traitValues[i]))
+				elif a1 == 1.0:
+					if b1 == -1.0:
+						DB.append((thisstrain, traitValues[i]))
+					elif b1 == 1.0:
+						DD.append((thisstrain, traitValues[i]))
+				else:
+					pass
+
+		#print BB, BD, DB, DD, max(iValues), min(iValues)
+
+		plotHeight = 400
+		plotWidth = 600
+		xLeftOffset = 60
+		xRightOffset = 40
+		yTopOffset = 40
+		yBottomOffset = 60
+
+		canvasHeight = plotHeight + yTopOffset + yBottomOffset
+		canvasWidth = plotWidth + xLeftOffset + xRightOffset
+		canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight))
+		XXX = [('Mat/Mat', BB), ('Mat/Pat', BD), ('Pat/Mat', DB), ('Pat/Pat', DD)]
+		XLabel = "Interval 1 / Interval 2"
+
+		if plotType == "Box":
+			Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel = XLabel)
+		else:
+			#Could be a separate function, but seems no other uses
+			max_Y = max(iValues)
+			min_Y = min(iValues)
+			scaleY = Plot.detScale(min_Y, max_Y)
+			Yll = scaleY[0]
+			Yur = scaleY[1]
+			nStep = scaleY[2]
+			stepY = (Yur - Yll)/nStep
+			stepYPixel = plotHeight/(nStep)
+			canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset)
+
+			##draw Y Scale
+			YYY = Yll
+			YCoord = plotHeight + yTopOffset
+			scaleFont=pid.Font(ttf="cour",size=11,bold=1)
+			for i in range(nStep+1):
+				strY = Plot.cformat(d=YYY, rank=0)
+				YCoord = max(YCoord, yTopOffset)
+				canvas.drawLine(xLeftOffset,YCoord,xLeftOffset-5,YCoord)
+				canvas.drawString(strY,	xLeftOffset -30,YCoord +5,font=scaleFont)
+				YYY += stepY
+				YCoord -= stepYPixel
+
+
+			##draw X Scale
+			stepX = plotWidth/len(XXX)
+			XCoord = xLeftOffset + 0.5*stepX
+			YCoord = plotHeight + yTopOffset
+			scaleFont = pid.Font(ttf="tahoma",size=12,bold=0)
+			labelFont = pid.Font(ttf="tahoma",size=13,bold=0)
+			for item in XXX:
+				itemname, itemvalue = item
+				canvas.drawLine(XCoord, YCoord,XCoord, YCoord+5, color=pid.black)
+				canvas.drawString(itemname, XCoord - canvas.stringWidth(itemname,font=labelFont)/2.0,YCoord +20,font=labelFont)
+				itemvalue.sort(webqtlUtil.cmpOrder2)
+				j = 0
+				for item2 in itemvalue:
+					tstrain, tvalue = item2
+					canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5)
+					if j % 2 == 0:
+						canvas.drawString(tstrain, XCoord+5, plotHeight + yTopOffset - \
+						(tvalue-Yll)*plotHeight/(Yur - Yll) +5, font=scaleFont, color=pid.blue)
+					else:
+						canvas.drawString(tstrain, XCoord-canvas.stringWidth(tstrain,font=scaleFont)-5, \
+						plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll) +5, font=scaleFont, color=pid.blue)
+					j += 1
+				XCoord += stepX
+
+
+			labelFont=pid.Font(ttf="verdana",size=18,bold=0)
+			canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, YCoord +40, font=labelFont)
+			canvas.drawString("Value",xLeftOffset-40,  YCoord-(plotHeight -canvas.stringWidth("Value",font=labelFont))/2.0, font=labelFont, angle =90)
+
+
+		filename= webqtlUtil.genRandStr("Cate_")
+		canvas.save(webqtlConfig.IMGDIR+filename, format='gif')
+		img=HT.Image('/image/'+filename+'.gif',border=0)
+
+		TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign='top')
+		TD_LR.append(main_title, HT.Center(img))#, traitValues , len(traitValues), traitStrains, len(traitStrains), len(fd.genotype.prgy))
+		#TD_LR.append(main_title, HT.BR(), flanka1, flanka2, chram, HT.BR(), flankb1, flankb2, chrbm)
+		self.dict['body'] = str(TD_LR)
+
+
+