Merge branch 'flask' of http://github.com/zsloan/genenetwork

1 files changed, 1283 insertions, 0 deletions

diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
new file mode 100755
index 00000000..51a57a6d
--- /dev/null
+++ b/wqflask/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 __future__ import print_function
+
+from pprint import pformat as pf
+
+print("Lysol")
+
+from math import *
+import random
+import sys, os
+from numarray import linear_algebra as la
+from numarray import ones, array, dot, swapaxes
+
+import reaper
+sys.path.append("..")
+print(sys.path)
+from basicStatistics import corestats
+
+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):
+    """Obsolete - use percentile in corestats instead"""
+    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 find_outliers(vals):
+    """Calculates the upper and lower bounds of a set of sample/case values
+    
+    
+    >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537])
+    (11.252500000000001, 0.5364999999999993)
+    
+    >>> >>> find_outliers([9,12,15,17,31,50,7,5,6,8])
+    (32.0, -8.0)
+
+    If there are no vals, returns None for the upper and lower bounds,
+    which code that calls it will have to deal with.
+    >>> find_outliers([])
+    (None, None)
+    
+    """
+
+    print("xerxes vals is:", pf(vals))
+
+    if vals:
+        #print("vals is:", pf(vals))
+        stats = corestats.Stats(vals)
+        low_hinge = stats.percentile(25)
+        up_hinge = stats.percentile(75)
+        hstep = 1.5 * (up_hinge - low_hinge)
+
+        upper_bound = up_hinge + hstep
+        lower_bound = low_hinge - hstep
+
+    else:
+        upper_bound = None
+        lower_bound = None
+
+    print(pf(locals()))
+    return upper_bound, lower_bound
+
+
+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
+
+
+def _test():
+    import doctest
+    doctest.testmod()
+
+
+if __name__=="__main__":
+    _test()