Add all the source codes into the github.

1 files changed, 1283 insertions, 0 deletions

diff --git a/web/webqtl/utility/Plot.py b/web/webqtl/utility/Plot.py
new file mode 100755
index 00000000..2401c85c
--- /dev/null
+++ b/web/webqtl/utility/Plot.py
@@ -0,0 +1,1283 @@
+# 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