Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 1283 deletions

diff --git a/web/webqtl/utility/Plot.py b/web/webqtl/utility/Plot.py
deleted file mode 100755
index 2401c85c..00000000
--- a/web/webqtl/utility/Plot.py
+++ /dev/null
@@ -1,1283 +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 piddle as pid
-from math import *
-import random
-import sys, os
-from numarray import linear_algebra as la
-from numarray import ones, array, dot, swapaxes
-
-import reaper
-
-import svg
-import webqtlUtil
-from base import webqtlConfig
-
-
-def cformat(d, rank=0):
-	'custom string format'
-	strD = "%2.6f" % d
-	
-	if rank == 0:
-		while strD[-1] in ('0','.'):
-			if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4:
-				break
-			elif strD[-1] == '.':
-				strD = strD[:-1]
-				break
-			else:
-				strD = strD[:-1]
-	
-	else:
-		strD = strD.split(".")[0]		
-
-	if strD == '-0.0':
-		strD = '0.0'
-	return strD
-	
-def frange(start, end=None, inc=1.0): 
-	"A faster range-like function that does accept float increments..." 
-	if end == None: 
-		end = start + 0.0 
-		start = 0.0 
-	else: 
-		start += 0.0 # force it to be a float 
-	count = int((end - start) / inc) 
-	if start + count * inc != end: 
-	# Need to adjust the count. AFAICT, it always comes up one short. 
-		count += 1 
-	L = [start] * count 
-	for i in xrange(1, count): 
-		L[i] = start + i * inc 
-	return L 
-
-
-def gammln(xx):
-	cof=[76.18009173,-86.50532033,24.01409822,-1.231739516,0.120858003e-2,-0.536382e-5]
-	x=xx-1.0
-	tmp=x+5.5
-	tmp -=(x+0.5)*log(tmp)
-	ser=1.0
-	for item in cof:
-		x+=1.0
-		ser+=item/x
-	
-	return -tmp+log(2.50662827465*ser)
-	
-
-def gser(a,x):
-	gln=gammln(a)
-	ITMAX=100
-	EPS=3.0e-7
-	
-	if x<=0.0:
-		gamser=0.0
-		return [gamser,gln]
-	else:
-		ap=a
-		sum=1.0/a
-		dele=sum
-		for i in range(1,ITMAX+1):
-			ap+=1.0
-			dele*=x/ap
-			sum+=dele
-			if abs(dele)<abs(sum)*EPS:
-				gamser=sum*exp(-x+a*log(x)-gln)
-				return [gamser,gln]
-	return None
-	
-def gcf(a,x):
-	ITMAX=100
-	EPS=3.0e-7
-	gold=0.0
-	fac=1
-	b1=1.0
-	b0=0.0
-	a0=1.0
-	gln=gammln(a)
-	
-	a1=x
-	for n in range(1,ITMAX+1):
-		an=n+0.0
-		ana=an-a
-		a0=(a1+a0*ana)*fac
-		b0=(b1+b0*ana)*fac
-		anf=an*fac
-		a1=x*a0+anf*a1
-		b1=x*b0+anf*b1
-		if (a1):
-			fac=1.0/a1
-			g=b1*fac
-			if abs((g-gold)/g)<EPS:
-				gammcf=exp(-x+a*log(x)-gln)*g
-				return [gammcf,gln]
-			gold=g
-	return None
-	
-def gammp(a,x):
-	if x<0.0 or a<=0.0:
-		return None
-	if x<(a+1.0):
-		a=gser(a,x)[0]
-		return a
-	else:
-		a=gcf(a,x)[0]
-		return 1.0-a
-def U(n):
-	x=pow(0.5,1.0/n)
-	m=[1-x]
-	for i in range(2,n):
-		a=(i-0.3175)/(n+0.365)
-		m.append(a)
-	m.append(x)
-	return m
-		
-def erf(x):
-	if x<0.0:
-		return -gammp(0.5,x*x)
-	else:
-		return gammp(0.5,x*x)
-
-def erfcc(x):
-	z=abs(x)
-	t=1.0/(1.0+0.5*z)
-	ans=t*exp(-z*z-1.26551223+t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+t*(0.27886807+t*(-1.13520398+t*(1.48851587+t*(-0.82215223+t*0.17087277)))))))))
-	if x>=0.0:
-		return ans
-	else:
-		return 2.0-ans
-		
-def calMeanVar(data):
-	n=len(data)
-	if n<2:
-		return None
-	else:
-		sum=reduce(lambda x,y:x+y,data,0.0)
-		mean=sum/n
-		z=data[:]
-		for i in range(n):
-			z[i]=z[i]-mean
-		variance=reduce(lambda x,y:x+y*y,z,0.0)
-		variance /= n-1
-		variance =sqrt(variance)
-		for i in range(n):
-			z[i]=z[i]/variance
-		return z
-		
-def inverseCumul(p):
-	#Coefficients in rational approximations.
-	a = [-3.969683028665376e+01,2.209460984245205e+02,-2.759285104469687e+02,1.383577518672690e+02,-3.066479806614716e+01,2.506628277459239e+00]
-
-	b = [-5.447609879822406e+01,1.615858368580409e+02,-1.556989798598866e+02,6.680131188771972e+01,-1.328068155288572e+01]
-
-	c = [-7.784894002430293e-03,-3.223964580411365e-01,-2.400758277161838e+00,-2.549732539343734e+00,4.374664141464968e+00,2.938163982698783e+00]
-
-	d =  [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00]
-
-	#Define break-points.
-
-	p_low  = 0.02425
-	p_high = 1 - p_low
-
-	#Rational approximation for lower region.
-
-	if p > 0 and p < p_low:
-   		q = sqrt(-2*log(p))
-   		x = (((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) / ((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
-
-
-	#Rational approximation for central region.
-
-	elif p>= p_low and p <= p_high:
-   		q = p - 0.5
-   		r = q*q
-   		x = (((((a[0]*r+a[1])*r+a[2])*r+a[3])*r+a[4])*r+a[5])*q /(((((b[0]*r+b[1])*r+b[2])*r+b[3])*r+b[4])*r+1)
-
-	#Rational approximation for upper region.
-
-	elif p>p_high and  p < 1:
-   		q = sqrt(-2*log(1-p))
-   		x = -(((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) /((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
-
-	else:
-		return None
-
-	if p>0 and p < 1:
-   		e = 0.5 * erfcc(-x/sqrt(2)) - p 
-   		u = e * sqrt(2*pi) * exp(x*x/2)
-   		x = x - u/(1 + x*u/2)
-		return x
-	else:
-		return None
-
-def gmean(lst):
-	N = len(lst)
-	if N == 0:
-		return 0
-	else:
-		return (reduce(lambda x,y: x+y, lst, 0.0))/N
-
-def gmedian(lst2):
-	lst = lst2[:]
-	N = len(lst)
-	if N == 0:
-		return 0
-	else:
-		lst.sort()
-		if N % 2 == 0:
-			return (lst[N/2]+lst[(N-2)/2])/2.0
-		else:
-			return lst[(N-1)/2]
-			
-def gpercentile(lst2, np):
-	lst = lst2[:]
-	N = len(lst)
-	if N == 0 or np > 100 or np < 0:
-		return None
-	else:
-		lst.sort()
-		pNadd1 = (np/100.0)*N
-		k = int(pNadd1)
-		d = pNadd1 - k
-		if k == 0:
-			return lst[0]
-		elif k >= N-1:
-			return lst[N-1]
-		else:
-			return lst[k-1] + d*(lst[k] - lst[k-1])
-		
-def findOutliers(vals):
-	
-	valsOnly = []
-	dataXZ = vals[:]
-	for i in range(len(dataXZ)):
-		valsOnly.append(dataXZ[i][1])
-		
-	data = [('', valsOnly[:])]	
-	
-	for item in data:
-		itemvalue = item[1]
-		nValue = len(itemvalue)
-		catValue = []
-		
-		for item2 in itemvalue:
-			try:
-				tstrain, tvalue = item2
-			except:
-				tvalue = item2
-			if nValue <= 4:
-				continue
-			else:
-				catValue.append(tvalue)
-				
-		if catValue != []:
-			lowHinge = gpercentile(catValue, 25)
-			upHinge = gpercentile(catValue, 75)
-			Hstep = 1.5*(upHinge - lowHinge)
-			
-			outlier = []
-			extreme = []
-			
-			upperBound = upHinge + Hstep
-			lowerBound = lowHinge - Hstep
-			
-			for item in catValue:
-				if item >= upHinge + 2*Hstep:
-					extreme.append(item)
-				elif item >= upHinge + Hstep:
-					outlier.append(item)
-				else:
-					pass
-				
-			for item in catValue:
-				if item <= lowHinge - 2*Hstep:
-					extreme.append(item)
-				elif item <= lowHinge - Hstep:
-					outlier.append(item)
-				else:
-					pass
-		else:
-			upperBound = 1000
-			lowerBound = -1000
-				
-	return upperBound, lowerBound
-					
-					
-def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabel="Value"):
-	xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-	plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-	plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-	iValues = []
-	for item in data:
-		for item2 in item[1]:
-			try:
-				iValues.append(item2[1])
-			except:
-				iValues.append(item2)
-	
-	#draw frame		
-	max_Y = max(iValues)
-	min_Y = min(iValues)
-	scaleY = 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 = 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(data)
-	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 data:
-		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)
-		
-		nValue = len(itemvalue)
-		catValue = []
-		for item2 in itemvalue:
-			try:
-				tstrain, tvalue = item2
-			except:
-				tvalue = item2
-			if nValue <= 4:
-				canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5)
-			else:
-				catValue.append(tvalue)
-		if catValue != []:
-			catMean = gmean(catValue)
-			catMedian = gmedian(catValue)
-			lowHinge = gpercentile(catValue, 25)
-			upHinge = gpercentile(catValue, 75)
-			Hstep = 1.5*(upHinge - lowHinge)
-			
-			outlier = []
-			extrem = []
-			
-			upperAdj = None
-			for item in catValue:
-				if item >= upHinge + 2*Hstep:
-					extrem.append(item)
-				elif item >= upHinge + Hstep:
-					outlier.append(item)
-				elif item > upHinge and  item < upHinge + Hstep:
-					if upperAdj == None or item > upperAdj:
-						upperAdj = item
-				else:
-					pass
-			lowerAdj = None
-			for item in catValue:
-				if item <= lowHinge - 2*Hstep:
-					extrem.append(item)
-				elif item <= lowHinge - Hstep:
-					outlier.append(item)
-				if item < lowHinge and  item > lowHinge - Hstep:
-					if lowerAdj == None or item < lowerAdj:
-						lowerAdj = item
-					else:
-						pass
-			canvas.drawRect(XCoord-20, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
-				XCoord+20, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll))
-			canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll), \
-				XCoord+20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll))
-			if upperAdj != None:
-				canvas.drawLine(XCoord, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll), \
-				XCoord, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
-				canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll), \
-				XCoord+20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
-			if lowerAdj != None:
-				canvas.drawLine(XCoord, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
-				XCoord, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
-				canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll), \
-				XCoord+20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
-			
-			outlierFont = pid.Font(ttf="cour",size=12,bold=0)
-			if outlier != []:
-				for item in outlier:
-					yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
-					#canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
-					canvas.drawString('o', XCoord-3, yc+5, font=outlierFont, color=pid.orange)
-			if extrem != []:
-				for item in extrem:
-					yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
-					#canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
-					canvas.drawString('*', XCoord-3, yc+6, font=outlierFont, color=pid.red)
-			
-			canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \
-				color=pid.blue,size=3)
-			#print (catMean, catMedian, cat25per, cat75per)
-			pass
-		
-		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(YLabel,xLeftOffset-40, YCoord-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0,\
-	 font=labelFont, angle =90)
-
-def plotSecurity(canvas, text="12345"):
-	if not text:
-		return
-
-	plotWidth = canvas.size[0]
-	plotHeight = canvas.size[1]
-	if plotHeight<=0 or plotWidth<=0:
-		return
-		
-	bgColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random())
-	canvas.drawRect(0,0,plotWidth,plotHeight, edgeColor=bgColor, fillColor=bgColor)
-	
-	for i in range(30):
-		randomColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random())
-		scaleFont=pid.Font(ttf="cour",size=random.choice(range(20, 50)))
-		canvas.drawString(random.choice('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'), 
-			int(random.random()*plotWidth), int(random.random()*plotHeight), font=scaleFont, 
-			color=randomColor, angle=random.choice(range(-45, 50)))
-			
-	step = (plotWidth-20)/len(text)
-	startX = 20
-	for item in text:
-		randomColor = pid.Color(0.6*random.random(),0.6*random.random(), 0.6*random.random())
-		scaleFont=pid.Font(ttf="verdana",size=random.choice(range(50, 60)),bold=1)
-		canvas.drawString(item, startX, plotHeight/2-10, font=scaleFont, 
-			color=randomColor, angle=random.choice(range(-45, 50)))
-		startX += step
- 
-# parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py)
-# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py)	 
-def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
-	
-	xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-	
-	plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-	plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-	if plotHeight<=0 or plotWidth<=0:
-		return
-		
-	if len(data) < 2:
-		return
-		
-	max_D = max(data)
-	min_D = min(data)
-	#add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
-	if max_D == float('inf') or max_D>webqtlConfig.MAXLRS:
-		max_D=webqtlConfig.MAXLRS #maximum LRS value
-		
-	xLow, xTop, stepX = detScale(min_D, max_D)
-	
-	#reduce data
-	step = ceil((xTop-xLow)/50.0)
-	j = xLow
-	dataXY = []
-	Count = []
-	while j <= xTop:
-		dataXY.append(j)
-		Count.append(0)
-		j += step 
-	
-	for i, item in enumerate(data):
-		if item == float('inf') or item>webqtlConfig.MAXLRS:
-			item = webqtlConfig.MAXLRS #maximum LRS value
-		j = int((item-xLow)/step)
-		Count[j] += 1	
-		
-	yLow, yTop, stepY=detScale(0,max(Count))
-	
-	#draw data
-	xScale = plotWidth/(xTop-xLow)
-	yScale = plotHeight/(yTop-yLow)
-	barWidth = xScale*step
-	
-	for i, count in enumerate(Count):
-		if count:
-			xc = (dataXY[i]-xLow)*xScale+xLeftOffset
-			yc =-(count-yLow)*yScale+yTopOffset+plotHeight
-			canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor)
-	
-	#draw drawing region
-	canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
-
-	#draw scale
-	scaleFont=pid.Font(ttf="cour",size=11,bold=1)
-	x=xLow
-	for i in range(stepX+1):
-		xc=xLeftOffset+(x-xLow)*xScale
-		canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor)
-		strX = cformat(d=x, rank=0)
-		canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont)
-		x+= (xTop - xLow)/stepX
-		
-	y=yLow
-	for i in range(stepY+1):
-		yc=yTopOffset+plotHeight-(y-yLow)*yScale
-		canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
-		strY = "%d" %y
-		canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
-		y+= (yTop - yLow)/stepY
-	
-	#draw label
-	labelFont=pid.Font(ttf="tahoma",size=17,bold=0)
-	if XLabel:
-		canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
-			yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor)
-	
-	if YLabel:
-		canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
-			font=labelFont,color=labelColor,angle=90)
-
-	labelFont=pid.Font(ttf="verdana",size=16,bold=0)
-	if title:
-		canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
-			20,font=labelFont,color=labelColor)
-
-def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, sLabel = None, offset= (80, 20, 40, 100), barSpace = 2, zoom = 1):
-	xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-	plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-	plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-	if plotHeight<=0 or plotWidth<=0:
-		return
-	
-	NNN = len(data)
-	if NNN < 2 or NNN != len(label):
-		return
-	if variance and len(variance)!=NNN:
-		variance = []
-	
-	Y2 = data[:]
-	if variance:
-		for i in range(NNN):
-			if variance[i]:
-				Y2 += [data[i]-variance[i]]
-				
-	#Y axis
-	YLow, YTop, stepY = detScale(min(Y2), max(Y2))
-	YScale = plotHeight/(YTop - YLow)
-	
-	if YLow < 0  and  YTop > 0:
-		drawZero = 1
-	else:
-		drawZero = 0
-		
-	#X axis
-	X = range(NNN)
-	Xll= 0 
-	Xur= NNN-1
-	
-	
-	if drawZero:
-		YZero = yTopOffset+plotHeight-YScale*(0-YLow)
-		canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero)
-	else:
-		YZero = yTopOffset+plotHeight
-	#draw data
-	spaceWidth = barSpace
-	if spaceWidth < 1:
-		spaceWidth = 1
-	barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN)
-	
-	xc= xLeftOffset
-	scaleFont=pid.Font(ttf="verdana",size=11,bold=0)	
-	for i in range(NNN):
-		yc = yTopOffset+plotHeight-(data[i]-YLow)*YScale
-		canvas.drawRect(xc,YZero,xc+barWidth-1, yc, edgeColor=barColor,fillColor=barColor)
-		if variance and variance[i]:
-			varlen = variance[i]*YScale
-			if yc-varlen < yTopOffset:
-				topYd = yTopOffset
-			else:
-				topYd = yc-varlen
-				canvas.drawLine(xc+barWidth/2-2,yc-varlen,xc+barWidth/2+2,yc-varlen,color=pid.red)
-			canvas.drawLine(xc+barWidth/2,yc+varlen,xc+barWidth/2,topYd,color=pid.red)
-			canvas.drawLine(xc+barWidth/2-2,yc+varlen,xc+barWidth/2+2,yc+varlen,color=pid.red)
-		strX = label[i]
-		canvas.drawString(strX,xc+barWidth/2.0+2,yTopOffset+plotHeight+2+canvas.stringWidth(strX,font=scaleFont),font=scaleFont,angle=90)
-		xc += barWidth + spaceWidth	
-		
-	#draw drawing region
-	canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
-	
-	#draw Y scale
-	scaleFont=pid.Font(ttf="cour",size=16,bold=1)		
-	y=YLow
-	for i in range(stepY+1):
-		yc=yTopOffset+plotHeight-(y-YLow)*YScale
-		canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
-		strY = cformat(d=y, rank=0)
-		canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
-		y+= (YTop - YLow)/stepY
-	
-	#draw label
-	labelFont=pid.Font(ttf="verdana",size=17,bold=0)
-	if XLabel:
-		canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,yTopOffset+plotHeight+65,font=labelFont,color=labelColor)
-	
-	if YLabel:
-		canvas.drawString(YLabel,xLeftOffset-50, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,font=labelFont,color=labelColor,angle=90)
-	
-	labelFont=pid.Font(ttf="verdana",size=18,bold=0)
-	if title:
-		canvas.drawString(title,xLeftOffset,yTopOffset-15,font=labelFont,color=labelColor)
-		
-	return
-		
-def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, axesColor=pid.black, labelColor=pid.black, lineSize="thin", lineColor=pid.grey, idFont="arial", idColor=pid.blue, idSize="14", symbolColor=pid.black, symbolType="circle", filled="yes", symbolSize="tiny", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1, bufferSpace = 15):
-	'displayR : correlation scatter plot, loadings : loading plot'
-	
-	dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX))
-		
-	#get ID font size
-	idFontSize = int(idSize)	
-	
-	#If filled is yes, set fill color
-	if filled == "yes":
-		fillColor = symbolColor
-	else:
-		fillColor = None	
-	
-	if symbolSize == "large":
-		sizeModifier = 7
-		fontModifier = 12
-	elif symbolSize == "medium":
-		sizeModifier = 5
-		fontModifier = 8
-	elif symbolSize == "small":
-		sizeModifier = 3
-		fontModifier = 3
-	else:
-		sizeModifier = 1
-		fontModifier = -1	
-			
-	if rank == 0:    # Pearson correlation
-		bufferSpace = 0
-		dataXPrimary = dataX
-		dataYPrimary = dataY
-		dataXAlt = dataXRanked    #Values used just for printing the other corr type to the graph image
-		dataYAlt = dataYRanked    #Values used just for printing the other corr type to the graph image
-	else:    # Spearman correlation: Switching Ranked and Unranked X and Y values
-		dataXPrimary = dataXRanked
-		dataYPrimary = dataYRanked
-		dataXAlt = dataX    #Values used just for printing the other corr type to the graph image
-		dataYAlt = dataY    #Values used just for printing the other corr type to the graph image
-	
-	xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-	plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-	plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-	if plotHeight<=0 or plotWidth<=0:
-		return
-	if len(dataXPrimary) < 1 or  len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)):
-		return
-	
-	max_X=max(dataXPrimary)
-	min_X=min(dataXPrimary)
-	max_Y=max(dataYPrimary)
-	min_Y=min(dataYPrimary)
-	
-	#for some reason I forgot why I need to do this
-	if loadingPlot:
-		min_X = min(-0.1,min_X)
-		max_X = max(0.1,max_X)
-		min_Y = min(-0.1,min_Y)
-		max_Y = max(0.1,max_Y)
-	
-	xLow, xTop, stepX=detScale(min_X,max_X)
-	yLow, yTop, stepY=detScale(min_Y,max_Y)
-	xScale = plotWidth/(xTop-xLow)
-	yScale = plotHeight/(yTop-yLow)
-	
-	#draw drawing region
-	canvas.drawRect(xLeftOffset-bufferSpace, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace)
-	canvas.drawRect(xLeftOffset-bufferSpace+1, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace-1)
-
-	#calculate data points	
-	data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary)
-	xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary)
-
-	labelFont=pid.Font(ttf=idFont,size=idFontSize,bold=0)
-
-	if loadingPlot:
-		xZero = -xLow*xScale+xLeftOffset
-		yZero = yTopOffset+plotHeight+yLow*yScale
-		for point in xCoord:
-			canvas.drawLine(xZero,yZero,point[0],point[1],color=pid.red)
-	else:
-		if connectdot:
-			canvas.drawPolygon(xCoord,edgeColor=plotColor,closed=0)
-		else:
-			pass
-
-	symbolFont = pid.Font(ttf="fnt_bs", size=12+fontModifier,bold=0)
-
-	for i, item in enumerate(xCoord):
-		if dataLabel and dataLabel[i] in specialCases:
-			canvas.drawRect(item[0]-3, item[1]-3, item[0]+3, item[1]+3, edgeColor=pid.green)
-			#canvas.drawCross(item[0],item[1],color=pid.blue,size=5)
-		else:
-			if symbolType == "vertRect":
-				canvas.drawRect(x1=item[0]-sizeModifier+2,y1=item[1]-sizeModifier-2, x2=item[0]+sizeModifier-1,y2=item[1]+sizeModifier+2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
-			elif (symbolType == "circle" and filled != "yes"):
-				canvas.drawString(":", item[0]-canvas.stringWidth(":",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont)
-			elif (symbolType == "circle" and filled == "yes"):
-				canvas.drawString("5", item[0]-canvas.stringWidth("5",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont)
-			elif symbolType == "horiRect":
-				canvas.drawRect(x1=item[0]-sizeModifier-1,y1=item[1]-sizeModifier+3, x2=item[0]+sizeModifier+3,y2=item[1]+sizeModifier-2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
-			elif (symbolType == "square"):
-				canvas.drawRect(x1=item[0]-sizeModifier+1,y1=item[1]-sizeModifier-4, x2=item[0]+sizeModifier+2,y2=item[1]+sizeModifier-3, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
-			elif (symbolType == "diamond" and filled != "yes"):
-				canvas.drawString(",", item[0]-canvas.stringWidth(",",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor)
-			elif (symbolType == "diamond" and filled == "yes"):
-				canvas.drawString("D", item[0]-canvas.stringWidth("D",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor)	
-			elif symbolType == "4-star":
-				canvas.drawString("l", item[0]-canvas.stringWidth("l",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor)	
-			elif symbolType == "3-star":
-				canvas.drawString("k", item[0]-canvas.stringWidth("k",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor)	
-			else:	
-				canvas.drawCross(item[0],item[1]-2,color=symbolColor, size=sizeModifier+2)
-
-		if showLabel and dataLabel:
-			if (symbolType == "vertRect" or symbolType == "diamond"):
-				labelGap = 15
-			elif (symbolType == "4-star" or symbolType == "3-star"):
-				labelGap = 12
-			else:
-			    labelGap = 11
-			canvas.drawString(dataLabel[i], item[0]- canvas.stringWidth(dataLabel[i],
-				font=labelFont)/2 + 1, item[1]+(labelGap+sizeModifier+(idFontSize-12)), font=labelFont, color=idColor)
-                        	
-	#draw scale
-	scaleFont=pid.Font(ttf="cour",size=16,bold=1)
-	
-
-	x=xLow
-	for i in range(stepX+1):
-		xc=xLeftOffset+(x-xLow)*xScale
-		if ((x == 0) & (rank == 1)):
-			pass
-		else:
-			canvas.drawLine(xc,yTopOffset+plotHeight + bufferSpace,xc,yTopOffset+plotHeight+5 + bufferSpace, color=axesColor)		
-		strX = cformat(d=x, rank=rank)
-		if ((strX == "0") & (rank == 1)):
-			pass
-		else:
-			canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+20 + bufferSpace,font=scaleFont)
-		x+= (xTop - xLow)/stepX
-	
-	y=yLow
-	for i in range(stepY+1):
-		yc=yTopOffset+plotHeight-(y-yLow)*yScale
-		if ((y == 0) & (rank == 1)):
-			pass
-		else:
-			canvas.drawLine(xLeftOffset - bufferSpace,yc,xLeftOffset-5 - bufferSpace,yc, color=axesColor)
-		strY = cformat(d=y, rank=rank)
-		if ((strY == "0") & (rank == 1)):
-			pass
-		else:
-			canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)- 10 - bufferSpace,yc+4,font=scaleFont)
-		y+= (yTop - yLow)/stepY
-			
-	#draw label
-
-	labelFont=pid.Font(ttf="verdana",size=canvas.size[0]/45,bold=0)
-	titleFont=pid.Font(ttf="verdana",size=canvas.size[0]/40,bold=0)
-		
-	if (rank == 1 and not title):
-		canvas.drawString("Spearman Rank Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Spearman Rank Correlation",font=titleFont))/2.0,
-						  25,font=titleFont,color=labelColor)
-	elif (rank == 0 and not title):
-		canvas.drawString("Pearson Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Pearson Correlation",font=titleFont))/2.0,
-						  25,font=titleFont,color=labelColor)
-		
-	if XLabel:
-		canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
-			yTopOffset+plotHeight+yBottomOffset-25,font=labelFont,color=labelColor)
-	
-	if YLabel:
-		canvas.drawString(YLabel, xLeftOffset-65, yTopOffset+plotHeight- (plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
-			font=labelFont,color=labelColor,angle=90)
-
-	labelFont=pid.Font(ttf="verdana",size=20,bold=0)
-	if title:
-		canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
-			20,font=labelFont,color=labelColor)
-	
-	if fitcurve:
-		import sys
-		sys.argv = [ "mod_python" ]
-		#from numarray import linear_algebra as la
-		#from numarray import ones, array, dot, swapaxes
-		fitYY = array(dataYPrimary)
-		fitXX = array([ones(len(dataXPrimary)),dataXPrimary])
-		AA = dot(fitXX,swapaxes(fitXX,0,1))
-		BB = dot(fitXX,fitYY)
-		bb = la.linear_least_squares(AA,BB)[0]
-		
-		xc1 = xLeftOffset
-		yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale 
-		if yc1 > yTopOffset+plotHeight:
-			yc1 = yTopOffset+plotHeight
-			xc1 = (yLow-bb[0])/bb[1]
-			xc1=(xc1-xLow)*xScale+xLeftOffset
-		elif yc1 < yTopOffset:
-			yc1 = yTopOffset
-			xc1 = (yTop-bb[0])/bb[1]
-			xc1=(xc1-xLow)*xScale+xLeftOffset
-		else:
-			pass
-		
-		xc2 = xLeftOffset + plotWidth 
-		yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
-		if yc2 > yTopOffset+plotHeight:
-			yc2 = yTopOffset+plotHeight
-			xc2 = (yLow-bb[0])/bb[1]
-			xc2=(xc2-xLow)*xScale+xLeftOffset
-		elif yc2 < yTopOffset:
-			yc2 = yTopOffset
-			xc2 = (yTop-bb[0])/bb[1]
-			xc2=(xc2-xLow)*xScale+xLeftOffset
-		else:
-			pass
-
-		canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace,xc2,yc2,color=lineColor)
-		if lineSize == "medium":
-			canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor)
-		if lineSize == "thick":
-			canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor)
-			canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace-1,xc2,yc2-1,color=lineColor)
-		
-		
-	if displayR:
-		labelFont=pid.Font(ttf="trebuc",size=canvas.size[0]/60,bold=0)
-		NNN = len(dataX)
-		corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0]
-
-		if NNN < 3:
-			corrPValue = 1.0
-		else:
-			if abs(corr) >= 1.0:
-				corrPValue = 0.0
-			else:
-				ZValue = 0.5*log((1.0+corr)/(1.0-corr))
-				ZValue = ZValue*sqrt(NNN-3)
-				corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-				
-		NStr = "N = %d" % NNN
-		strLenN = canvas.stringWidth(NStr,font=labelFont)
-
-		if rank == 1:
-		    if corrPValue < 0.0000000000000001:
-				corrStr = "Rho = %1.3f P < 1.00 E-16" % (corr)
-		    else:
-				corrStr = "Rho = %1.3f P = %3.2E" % (corr, corrPValue)
-		else:
-		    if corrPValue < 0.0000000000000001:
-				corrStr = "r = %1.3f P < 1.00 E-16" % (corr)
-		    else:
-				corrStr = "r = %1.3f P = %3.2E" % (corr, corrPValue)
-		strLen = canvas.stringWidth(corrStr,font=labelFont)
-
-		canvas.drawString(NStr,xLeftOffset,yTopOffset-10,font=labelFont,color=labelColor)
-		canvas.drawString(corrStr,xLeftOffset+plotWidth-strLen,yTopOffset-10,font=labelFont,color=labelColor)
-
-	return xCoord
-
-def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black", axesColor="black", labelColor="black", symbolColor="red", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1):
-	'displayR : correlation scatter plot, loadings : loading plot'
-	
-	dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX))
-			
-	# Switching Ranked and Unranked X and Y values if a Spearman Rank Correlation			
-	if rank == 0:
-		dataXPrimary = dataX
-		dataYPrimary = dataY
-		dataXAlt = dataXRanked
-		dataYAlt = dataYRanked		
-	
-	else:	
-		dataXPrimary = dataXRanked
-		dataYPrimary = dataYRanked
-		dataXAlt = dataX
-		dataYAlt = dataY
-
-
-	
-	xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-	plotWidth = drawSpace.attributes['width'] - xLeftOffset - xRightOffset
-	plotHeight = drawSpace.attributes['height'] - yTopOffset - yBottomOffset
-	if plotHeight<=0 or plotWidth<=0:
-		return
-	if len(dataXPrimary) < 1 or  len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)):
-		return
-	
-	max_X=max(dataXPrimary)
-	min_X=min(dataXPrimary)
-	max_Y=max(dataYPrimary)
-	min_Y=min(dataYPrimary)
-	
-	#for some reason I forgot why I need to do this
-	if loadingPlot:
-		min_X = min(-0.1,min_X)
-		max_X = max(0.1,max_X)
-		min_Y = min(-0.1,min_Y)
-		max_Y = max(0.1,max_Y)
-	
-	xLow, xTop, stepX=detScale(min_X,max_X)
-	yLow, yTop, stepY=detScale(min_Y,max_Y)
-	xScale = plotWidth/(xTop-xLow)
-	yScale = plotHeight/(yTop-yLow)
-	
-	#draw drawing region
-	r = svg.rect(xLeftOffset, yTopOffset, plotWidth,  plotHeight, 'none', axesColor, 1)
-	drawSpace.addElement(r)
-	
-	#calculate data points	
-	data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary)
-	xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary)
-	labelFontF = "verdana"
-	labelFontS = 11
-	
-	if loadingPlot:
-		xZero = -xLow*xScale+xLeftOffset
-		yZero = yTopOffset+plotHeight+yLow*yScale
-		for point in xCoord:
-			drawSpace.addElement(svg.line(xZero,yZero,point[0],point[1], "red", 1))
-	else:
-		if connectdot:
-			pass
-			#drawSpace.drawPolygon(xCoord,edgeColor=plotColor,closed=0)
-		else:
-			pass
-			
-	for i, item in enumerate(xCoord):
-		if dataLabel and dataLabel[i] in specialCases:
-			drawSpace.addElement(svg.rect(item[0]-3, item[1]-3, 6, 6, "none", "green", 0.5))
-			#drawSpace.drawCross(item[0],item[1],color=pid.blue,size=5)
-		else:
-			drawSpace.addElement(svg.line(item[0],item[1]+5,item[0],item[1]-5,symbolColor,1))
-			drawSpace.addElement(svg.line(item[0]+5,item[1],item[0]-5,item[1],symbolColor,1))
-		if showLabel and dataLabel:
-			pass
-			drawSpace.addElement(svg.text(item[0], item[1]+14, dataLabel[i], labelFontS, 
-				labelFontF, text_anchor="middle", style="stroke:blue;stroke-width:0.5;"))
-			#canvas.drawString(, item[0]- canvas.stringWidth(dataLabel[i],
-			#	font=labelFont)/2, item[1]+14, font=labelFont, color=pid.blue)
-	
-	#draw scale
-	#scaleFont=pid.Font(ttf="cour",size=14,bold=1)
-	x=xLow
-	for i in range(stepX+1):
-		xc=xLeftOffset+(x-xLow)*xScale
-		drawSpace.addElement(svg.line(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, axesColor, 1))
-		strX = cformat(d=x, rank=rank)
-		drawSpace.addElement(svg.text(xc,yTopOffset+plotHeight+20,strX,13, "courier", text_anchor="middle"))
-		x+= (xTop - xLow)/stepX
-		
-	y=yLow
-	for i in range(stepY+1):
-		yc=yTopOffset+plotHeight-(y-yLow)*yScale
-		drawSpace.addElement(svg.line(xLeftOffset,yc,xLeftOffset-5,yc, axesColor, 1))
-		strY = cformat(d=y, rank=rank)
-		drawSpace.addElement(svg.text(xLeftOffset-10,yc+5,strY,13, "courier", text_anchor="end"))
-		y+= (yTop - yLow)/stepY
-			
-	#draw label
-	labelFontF = "verdana"
-	labelFontS = 17
-	if XLabel:
-		drawSpace.addElement(svg.text(xLeftOffset+plotWidth/2.0,
-			yTopOffset+plotHeight+yBottomOffset-10,XLabel,
-			labelFontS, labelFontF, text_anchor="middle"))
-	
-	if YLabel:
-		drawSpace.addElement(svg.text(xLeftOffset-50,
-			 yTopOffset+plotHeight/2,YLabel,
-			labelFontS, labelFontF, text_anchor="middle", style="writing-mode:tb-rl", transform="rotate(270 %d %d)" % (xLeftOffset-50,  yTopOffset+plotHeight/2)))
-		#drawSpace.drawString(YLabel, xLeftOffset-50, yTopOffset+plotHeight- (plotHeight-drawSpace.stringWidth(YLabel,font=labelFont))/2.0,
-		#	font=labelFont,color=labelColor,angle=90)
-
-
-	if fitcurve:
-		sys.argv = [ "mod_python" ]
-                #from numarray import linear_algebra as la
-		#from numarray import ones, array, dot, swapaxes
-		fitYY = array(dataYPrimary)
-		fitXX = array([ones(len(dataXPrimary)),dataXPrimary])
-		AA = dot(fitXX,swapaxes(fitXX,0,1))
-		BB = dot(fitXX,fitYY)
-		bb = la.linear_least_squares(AA,BB)[0]
-		
-		xc1 = xLeftOffset
-		yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale 
-		if yc1 > yTopOffset+plotHeight:
-			yc1 = yTopOffset+plotHeight
-			xc1 = (yLow-bb[0])/bb[1]
-			xc1=(xc1-xLow)*xScale+xLeftOffset
-		elif yc1 < yTopOffset:
-			yc1 = yTopOffset
-			xc1 = (yTop-bb[0])/bb[1]
-			xc1=(xc1-xLow)*xScale+xLeftOffset
-		else:
-			pass
-		
-		xc2 = xLeftOffset + plotWidth 
-		yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
-		if yc2 > yTopOffset+plotHeight:
-			yc2 = yTopOffset+plotHeight
-			xc2 = (yLow-bb[0])/bb[1]
-			xc2=(xc2-xLow)*xScale+xLeftOffset
-		elif yc2 < yTopOffset:
-			yc2 = yTopOffset
-			xc2 = (yTop-bb[0])/bb[1]
-			xc2=(xc2-xLow)*xScale+xLeftOffset
-		else:
-			pass
-
-		drawSpace.addElement(svg.line(xc1,yc1,xc2,yc2,"green", 1))
-	
-	if displayR:		
-		labelFontF = "trebuc"
-		labelFontS = 14
-		NNN = len(dataX)
-
-		corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0]
-
-		if NNN < 3:
-			corrPValue = 1.0
-		else:
-			if abs(corr) >= 1.0:
-				corrPValue = 0.0
-			else:
-				ZValue = 0.5*log((1.0+corr)/(1.0-corr))
-				ZValue = ZValue*sqrt(NNN-3)
-				corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-				
-		NStr = "N of Cases=%d" % NNN
-		
-		if rank == 1:
-			corrStr = "Spearman's r=%1.3f P=%3.2E" % (corr, corrPValue)
-		else:
-			corrStr = "Pearson's r=%1.3f P=%3.2E" % (corr, corrPValue)
-		
-		drawSpace.addElement(svg.text(xLeftOffset,yTopOffset-10,NStr,
-			labelFontS, labelFontF, text_anchor="start"))
-		drawSpace.addElement(svg.text(xLeftOffset+plotWidth,yTopOffset-25,corrStr,
-			labelFontS, labelFontF, text_anchor="end"))
-	"""	
-	"""
-	return
-
-
-# This function determines the scale of the plot	
-def detScaleOld(min,max):
-	if min>=max:
-		return None
-	elif min == -1.0 and max == 1.0:
-		return [-1.2,1.2,12]
-	else:
-		a=max-min
-		b=floor(log10(a))
-		c=pow(10.0,b)
-		if a < c*5.0:
-			c/=2.0
-		#print a,b,c
-		low=c*floor(min/c)
-		high=c*ceil(max/c)
-		return [low,high,round((high-low)/c)]
-
-def detScale(min=0,max=0,bufferSpace=3):
-
-	if min>=max:
-		return None
-	elif min == -1.0 and max == 1.0:
-		return [-1.2,1.2,12]
-	else:
-		a=max-min
-		if max != 0:
-			max += 0.1*a
-		if min != 0:
-			if min > 0 and min < 0.1*a:
-				min = 0.0
-			else:
-				min -= 0.1*a
-		a=max-min
-		b=floor(log10(a))
-		c=pow(10.0,b)
-		low=c*floor(min/c)
-		high=c*ceil(max/c)
-		n = round((high-low)/c)
-		div = 2.0
-		while n < 5 or n > 15:
-			if n < 5:
-				c /= div
-			else:
-				c *= div
-			if div == 2.0:
-				div =5.0
-			else:
-				div =2.0
-			low=c*floor(min/c)
-			high=c*ceil(max/c)
-			n = round((high-low)/c)
-
-		return [low,high,n]
-
-
-
-def colorSpectrumOld(n):
-	if n == 1:
-		return [pid.Color(1,0,0)]
-	elif n == 2:
-		return [pid.Color(1,0,0),pid.Color(0,0,1)]
-	elif n == 3:
-		return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
-	else:
-		step = 2.0/(n-1)
-		red = 1.0
-		green = 0.0
-		blue = 0.0
-		colors = [pid.Color(red,green,blue)]
-		i = 1
-		greenpeak = 0
-		while i < n:
-			if red >= step:
-				red -= step
-				green += step
-				if green >= 1.0:
-					greenpeak = 1
-					blue += green -1.0
-					green = 1.0
-			else:
-				red = 0.0
-				if greenpeak:
-					green -= step
-					blue += step
-				else:
-					green += step
-				if green >= 1.0:
-					greenpeak = 1
-					blue += green -1.0
-					green = 2.0 -green
-				elif green < 0.0:
-					green = 0.0
-				else:
-					pass
-			colors.append(pid.Color(red,green,blue))
-			i += 1
-		return colors
-		
-		
-
-
-def bluefunc(x):
-	return 1.0 / (1.0 + exp(-10*(x-0.6)))
-
-
-def redfunc(x):
-	return 1.0 / (1.0 + exp(10*(x-0.5)))
-
-def greenfunc(x):
-	return 1 - pow(redfunc(x+0.2),2) - bluefunc(x-0.3)
-
-def colorSpectrum(n=100):
-	multiple = 10
-	if n == 1:
-		return [pid.Color(1,0,0)]
-	elif n == 2:
-		return [pid.Color(1,0,0),pid.Color(0,0,1)]
-	elif n == 3:
-		return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
-	N = n*multiple
-	out = [None]*N;
-	for i in range(N):
-		x = float(i)/N
-		out[i] = pid.Color(redfunc(x), greenfunc(x), bluefunc(x));
-	out2 = [out[0]]
-	step = N/float(n-1)
-	j = 0
-	for i in range(n-2):
-		j += step
-		out2.append(out[int(j)])
-	out2.append(out[-1])
-	return out2
-
-
-def colorSpectrumSVG(n=100):
-	multiple = 10
-	if n == 1:
-		return ["rgb(255,0,0)"]
-	elif n == 2:
-		return ["rgb(255,0,0)","rgb(0,0,255)"]
-	elif n == 3:
-		return ["rgb(255,0,0)","rgb(0,255,0)","rgb(0,0,255)"]
-	N = n*multiple
-	out = [None]*N;
-	for i in range(N):
-		x = float(i)/N
-		out[i] = "rgb(%d, %d, %d)" % (redfunc(x)*255, greenfunc(x)*255, bluefunc(x)*255);
-	out2 = [out[0]]
-	step = N/float(n-1)
-	j = 0
-	for i in range(n-2):
-		j += step
-		out2.append(out[int(j)])
-	out2.append(out[-1])
-	return out2
-
-
-def BWSpectrum(n=100):
-	multiple = 10
-	if n == 1:
-		return [pid.Color(0,0,0)]
-	elif n == 2:
-		return [pid.Color(0,0,0),pid.Color(1,1,1)]
-	elif n == 3:
-		return [pid.Color(0,0,0),pid.Color(0.5,0.5,0.5),pid.Color(1,1,1)]
-	
-	step = 1.0/n
-	x = 0.0
-	out = []
-	for i in range(n):
-		out.append(pid.Color(x,x,x));
-		x += step
-	return out