diff options
Diffstat (limited to 'wqflask/utility')
| -rwxr-xr-x | wqflask/utility/Plot.py | 868 |
1 files changed, 434 insertions, 434 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 04fe85bf..086f3d57 100755 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -487,440 +487,440 @@ def plotSecurity(canvas, text="12345"): # 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 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' |