def MidPointVariance(pos, parlist, klaw=PlainKolmogorovSpec2D): "Calculate the variance due to interpolation to form the mid-point" """ parlist : parent list """ # distances pos n=len(parlist) d= [ ((pos-x)**2).sum()**0.5 for x in parlist ] d=numarray.array(d) # Weights that make up the linear interpolation w = d/d.sum() poly = numarray.zeros(n, numarray.Float64) poly[0] = 1 poly -= w a,r=GenLinSystem(poly) # This is the factorisation which allows to directly substitude # the defining structure function into the equations. solution=la.linear_least_squares(a,r)[0] # distances between the supplied points parentdists=PairDists(parlist) varlist=[ klaw(x) for x in parentdists] varlist=numarray.array(varlist) interpvar= (varlist*solution).sum() p1toposdist= ((parlist[0]-pos)**2).sum() **0.5 requiredvar = klaw( p1toposdist) return requiredvar -interpvar
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
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