diff options
Diffstat (limited to 'wqflask/utility/Plot.py')
| -rwxr-xr-x | wqflask/utility/Plot.py | 334 |
1 files changed, 167 insertions, 167 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 2401c85c..e00b8e9e 100755 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -24,7 +24,7 @@ # # Last updated by GeneNetwork Core Team 2010/10/20 -import piddle as pid +#import piddle as pid from math import * import random import sys, os @@ -41,7 +41,7 @@ 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: @@ -51,29 +51,29 @@ def cformat(d, rank=0): break else: strD = strD[:-1] - + else: - strD = strD.split(".")[0] + 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 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): @@ -85,15 +85,15 @@ def gammln(xx): 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] @@ -109,7 +109,7 @@ def gser(a,x): gamser=sum*exp(-x+a*log(x)-gln) return [gamser,gln] return None - + def gcf(a,x): ITMAX=100 EPS=3.0e-7 @@ -119,7 +119,7 @@ def gcf(a,x): b0=0.0 a0=1.0 gln=gammln(a) - + a1=x for n in range(1,ITMAX+1): an=n+0.0 @@ -137,7 +137,7 @@ def gcf(a,x): return [gammcf,gln] gold=g return None - + def gammp(a,x): if x<0.0 or a<=0.0: return None @@ -155,7 +155,7 @@ def U(n): m.append(a) m.append(x) return m - + def erf(x): if x<0.0: return -gammp(0.5,x*x) @@ -170,7 +170,7 @@ def erfcc(x): return ans else: return 2.0-ans - + def calMeanVar(data): n=len(data) if n<2: @@ -187,7 +187,7 @@ def calMeanVar(data): 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] @@ -227,7 +227,7 @@ def inverseCumul(p): return None if p>0 and p < 1: - e = 0.5 * erfcc(-x/sqrt(2)) - p + 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 @@ -252,7 +252,7 @@ def gmedian(lst2): 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) @@ -269,21 +269,21 @@ def gpercentile(lst2, np): 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[:])] - + + data = [('', valsOnly[:])] + for item in data: itemvalue = item[1] nValue = len(itemvalue) catValue = [] - + for item2 in itemvalue: try: tstrain, tvalue = item2 @@ -293,18 +293,18 @@ def findOutliers(vals): 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) @@ -312,7 +312,7 @@ def findOutliers(vals): outlier.append(item) else: pass - + for item in catValue: if item <= lowHinge - 2*Hstep: extreme.append(item) @@ -323,10 +323,10 @@ def findOutliers(vals): 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 @@ -338,8 +338,8 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe iValues.append(item2[1]) except: iValues.append(item2) - - #draw frame + + #draw frame max_Y = max(iValues) min_Y = min(iValues) scaleY = detScale(min_Y, max_Y) @@ -349,7 +349,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe stepY = (Yur - Yll)/nStep stepYPixel = plotHeight/(nStep) canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset) - + ##draw Y Scale YYY = Yll YCoord = plotHeight + yTopOffset @@ -361,7 +361,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe 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 @@ -373,7 +373,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe 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: @@ -391,10 +391,10 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe 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: @@ -431,7 +431,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe 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: @@ -443,14 +443,14 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe 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) @@ -465,48 +465,48 @@ def plotSecurity(canvas, text="12345"): 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, + 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, + 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) +# 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 @@ -515,27 +515,27 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid while j <= xTop: dataXY.append(j) Count.append(0) - j += step - + 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 - + 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) @@ -548,7 +548,7 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid 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 @@ -556,13 +556,13 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid 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) @@ -578,34 +578,34 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor 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 + Xll= 0 Xur= NNN-1 - - + + if drawZero: YZero = yTopOffset+plotHeight-YScale*(0-YLow) canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero) @@ -616,9 +616,9 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor if spaceWidth < 1: spaceWidth = 1 barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN) - + xc= xLeftOffset - scaleFont=pid.Font(ttf="verdana",size=11,bold=0) + 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) @@ -633,13 +633,13 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor 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 - + 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) + scaleFont=pid.Font(ttf="cour",size=16,bold=1) y=YLow for i in range(stepY+1): yc=yTopOffset+plotHeight-(y-YLow)*YScale @@ -647,35 +647,35 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, 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) - + idFontSize = int(idSize) + #If filled is yes, set fill color if filled == "yes": fillColor = symbolColor else: - fillColor = None - + fillColor = None + if symbolSize == "large": sizeModifier = 7 fontModifier = 12 @@ -687,8 +687,8 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax fontModifier = 3 else: sizeModifier = 1 - fontModifier = -1 - + fontModifier = -1 + if rank == 0: # Pearson correlation bufferSpace = 0 dataXPrimary = dataX @@ -700,7 +700,7 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax 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 @@ -708,29 +708,29 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax 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 + #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) @@ -767,12 +767,12 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax 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) + 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) + 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.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: @@ -784,10 +784,10 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax 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): @@ -795,14 +795,14 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax if ((x == 0) & (rank == 1)): pass else: - canvas.drawLine(xc,yTopOffset+plotHeight + bufferSpace,xc,yTopOffset+plotHeight+5 + bufferSpace, color=axesColor) + 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 @@ -816,23 +816,23 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax 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) @@ -841,7 +841,7 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax 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" ] @@ -852,9 +852,9 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax 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 + yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale if yc1 > yTopOffset+plotHeight: yc1 = yTopOffset+plotHeight xc1 = (yLow-bb[0])/bb[1] @@ -865,8 +865,8 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax xc1=(xc1-xLow)*xScale+xLeftOffset else: pass - - xc2 = xLeftOffset + plotWidth + + xc2 = xLeftOffset + plotWidth yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale if yc2 > yTopOffset+plotHeight: yc2 = yTopOffset+plotHeight @@ -885,8 +885,8 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax 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) @@ -901,7 +901,7 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax 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) @@ -924,24 +924,24 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax 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 + + # 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: + 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 @@ -949,34 +949,34 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" 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 + + #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 @@ -988,7 +988,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" #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)) @@ -998,11 +998,11 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" 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, + 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 @@ -1012,7 +1012,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" 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 @@ -1020,7 +1020,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" 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 @@ -1028,7 +1028,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" 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, @@ -1046,9 +1046,9 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" 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 + yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale if yc1 > yTopOffset+plotHeight: yc1 = yTopOffset+plotHeight xc1 = (yLow-bb[0])/bb[1] @@ -1059,8 +1059,8 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" xc1=(xc1-xLow)*xScale+xLeftOffset else: pass - - xc2 = xLeftOffset + plotWidth + + xc2 = xLeftOffset + plotWidth yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale if yc2 > yTopOffset+plotHeight: yc2 = yTopOffset+plotHeight @@ -1074,8 +1074,8 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" pass drawSpace.addElement(svg.line(xc1,yc1,xc2,yc2,"green", 1)) - - if displayR: + + if displayR: labelFontF = "trebuc" labelFontS = 14 NNN = len(dataX) @@ -1091,24 +1091,24 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" 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 +# This function determines the scale of the plot def detScaleOld(min,max): if min>=max: return None @@ -1205,8 +1205,8 @@ def colorSpectrumOld(n): colors.append(pid.Color(red,green,blue)) i += 1 return colors - - + + def bluefunc(x): @@ -1273,7 +1273,7 @@ def BWSpectrum(n=100): 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 = [] |