# 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)=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