diff options
Diffstat (limited to 'wqflask/utility/Plot.py')
| -rwxr-xr-x | wqflask/utility/Plot.py | 1283 |
1 files changed, 1283 insertions, 0 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py new file mode 100755 index 00000000..51a57a6d --- /dev/null +++ b/wqflask/utility/Plot.py @@ -0,0 +1,1283 @@ +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See the GNU Affero General Public License for more details. +# +# This program is available from Source Forge: at GeneNetwork Project +# (sourceforge.net/projects/genenetwork/). +# +# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) +# at rwilliams@uthsc.edu and xzhou15@uthsc.edu +# +# +# +# This module is used by GeneNetwork project (www.genenetwork.org) +# +# Created by GeneNetwork Core Team 2010/08/10 +# +# Last updated by GeneNetwork Core Team 2010/10/20 + +#import piddle as pid + +from __future__ import print_function + +from pprint import pformat as pf + +print("Lysol") + +from math import * +import random +import sys, os +from numarray import linear_algebra as la +from numarray import ones, array, dot, swapaxes + +import reaper +sys.path.append("..") +print(sys.path) +from basicStatistics import corestats + +import svg +import webqtlUtil +from base import webqtlConfig + + +def cformat(d, rank=0): + 'custom string format' + strD = "%2.6f" % d + + if rank == 0: + while strD[-1] in ('0','.'): + if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4: + break + elif strD[-1] == '.': + strD = strD[:-1] + break + else: + strD = strD[:-1] + + else: + strD = strD.split(".")[0] + + if strD == '-0.0': + strD = '0.0' + return strD + +def frange(start, end=None, inc=1.0): + "A faster range-like function that does accept float increments..." + if end == None: + end = start + 0.0 + start = 0.0 + else: + start += 0.0 # force it to be a float + count = int((end - start) / inc) + if start + count * inc != end: + # Need to adjust the count. AFAICT, it always comes up one short. + count += 1 + L = [start] * count + for i in xrange(1, count): + L[i] = start + i * inc + return L + + +def gammln(xx): + cof=[76.18009173,-86.50532033,24.01409822,-1.231739516,0.120858003e-2,-0.536382e-5] + x=xx-1.0 + tmp=x+5.5 + tmp -=(x+0.5)*log(tmp) + ser=1.0 + for item in cof: + x+=1.0 + ser+=item/x + + return -tmp+log(2.50662827465*ser) + + +def gser(a,x): + gln=gammln(a) + ITMAX=100 + EPS=3.0e-7 + + if x<=0.0: + gamser=0.0 + return [gamser,gln] + else: + ap=a + sum=1.0/a + dele=sum + for i in range(1,ITMAX+1): + ap+=1.0 + dele*=x/ap + sum+=dele + if abs(dele)<abs(sum)*EPS: + gamser=sum*exp(-x+a*log(x)-gln) + return [gamser,gln] + return None + +def gcf(a,x): + ITMAX=100 + EPS=3.0e-7 + gold=0.0 + fac=1 + b1=1.0 + b0=0.0 + a0=1.0 + gln=gammln(a) + + a1=x + for n in range(1,ITMAX+1): + an=n+0.0 + ana=an-a + a0=(a1+a0*ana)*fac + b0=(b1+b0*ana)*fac + anf=an*fac + a1=x*a0+anf*a1 + b1=x*b0+anf*b1 + if (a1): + fac=1.0/a1 + g=b1*fac + if abs((g-gold)/g)<EPS: + gammcf=exp(-x+a*log(x)-gln)*g + return [gammcf,gln] + gold=g + return None + +def gammp(a,x): + if x<0.0 or a<=0.0: + return None + if x<(a+1.0): + a=gser(a,x)[0] + return a + else: + a=gcf(a,x)[0] + return 1.0-a +def U(n): + x=pow(0.5,1.0/n) + m=[1-x] + for i in range(2,n): + a=(i-0.3175)/(n+0.365) + m.append(a) + m.append(x) + return m + +def erf(x): + if x<0.0: + return -gammp(0.5,x*x) + else: + return gammp(0.5,x*x) + +def erfcc(x): + z=abs(x) + t=1.0/(1.0+0.5*z) + ans=t*exp(-z*z-1.26551223+t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+t*(0.27886807+t*(-1.13520398+t*(1.48851587+t*(-0.82215223+t*0.17087277))))))))) + if x>=0.0: + return ans + else: + return 2.0-ans + +def calMeanVar(data): + n=len(data) + if n<2: + return None + else: + sum=reduce(lambda x,y:x+y,data,0.0) + mean=sum/n + z=data[:] + for i in range(n): + z[i]=z[i]-mean + variance=reduce(lambda x,y:x+y*y,z,0.0) + variance /= n-1 + variance =sqrt(variance) + for i in range(n): + z[i]=z[i]/variance + return z + +def inverseCumul(p): + #Coefficients in rational approximations. + a = [-3.969683028665376e+01,2.209460984245205e+02,-2.759285104469687e+02,1.383577518672690e+02,-3.066479806614716e+01,2.506628277459239e+00] + + b = [-5.447609879822406e+01,1.615858368580409e+02,-1.556989798598866e+02,6.680131188771972e+01,-1.328068155288572e+01] + + c = [-7.784894002430293e-03,-3.223964580411365e-01,-2.400758277161838e+00,-2.549732539343734e+00,4.374664141464968e+00,2.938163982698783e+00] + + d = [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00] + + #Define break-points. + + p_low = 0.02425 + p_high = 1 - p_low + + #Rational approximation for lower region. + + if p > 0 and p < p_low: + q = sqrt(-2*log(p)) + x = (((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) / ((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1) + + + #Rational approximation for central region. + + elif p>= p_low and p <= p_high: + q = p - 0.5 + r = q*q + x = (((((a[0]*r+a[1])*r+a[2])*r+a[3])*r+a[4])*r+a[5])*q /(((((b[0]*r+b[1])*r+b[2])*r+b[3])*r+b[4])*r+1) + + #Rational approximation for upper region. + + elif p>p_high and p < 1: + q = sqrt(-2*log(1-p)) + x = -(((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) /((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1) + + else: + return None + + if p>0 and p < 1: + e = 0.5 * erfcc(-x/sqrt(2)) - p + u = e * sqrt(2*pi) * exp(x*x/2) + x = x - u/(1 + x*u/2) + return x + else: + return None + +def gmean(lst): + N = len(lst) + if N == 0: + return 0 + else: + return (reduce(lambda x,y: x+y, lst, 0.0))/N + +def gmedian(lst2): + lst = lst2[:] + N = len(lst) + if N == 0: + return 0 + else: + lst.sort() + if N % 2 == 0: + return (lst[N/2]+lst[(N-2)/2])/2.0 + else: + return lst[(N-1)/2] + +def gpercentile(lst2, np): + """Obsolete - use percentile in corestats instead""" + lst = lst2[:] + N = len(lst) + if N == 0 or np > 100 or np < 0: + return None + else: + lst.sort() + pNadd1 = (np/100.0)*N + k = int(pNadd1) + d = pNadd1 - k + if k == 0: + return lst[0] + elif k >= N-1: + return lst[N-1] + else: + return lst[k-1] + d*(lst[k] - lst[k-1]) + +def find_outliers(vals): + """Calculates the upper and lower bounds of a set of sample/case values + + + >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537]) + (11.252500000000001, 0.5364999999999993) + + >>> >>> find_outliers([9,12,15,17,31,50,7,5,6,8]) + (32.0, -8.0) + + If there are no vals, returns None for the upper and lower bounds, + which code that calls it will have to deal with. + >>> find_outliers([]) + (None, None) + + """ + + print("xerxes vals is:", pf(vals)) + + if vals: + #print("vals is:", pf(vals)) + stats = corestats.Stats(vals) + low_hinge = stats.percentile(25) + up_hinge = stats.percentile(75) + hstep = 1.5 * (up_hinge - low_hinge) + + upper_bound = up_hinge + hstep + lower_bound = low_hinge - hstep + + else: + upper_bound = None + lower_bound = None + + print(pf(locals())) + return upper_bound, lower_bound + + +def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabel="Value"): + xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset + plotWidth = canvas.size[0] - xLeftOffset - xRightOffset + plotHeight = canvas.size[1] - yTopOffset - yBottomOffset + iValues = [] + for item in data: + for item2 in item[1]: + try: + iValues.append(item2[1]) + except: + iValues.append(item2) + + #draw frame + max_Y = max(iValues) + min_Y = min(iValues) + scaleY = detScale(min_Y, max_Y) + Yll = scaleY[0] + Yur = scaleY[1] + nStep = scaleY[2] + stepY = (Yur - Yll)/nStep + stepYPixel = plotHeight/(nStep) + canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset) + + ##draw Y Scale + YYY = Yll + YCoord = plotHeight + yTopOffset + scaleFont=pid.Font(ttf="cour",size=11,bold=1) + for i in range(nStep+1): + strY = cformat(d=YYY, rank=0) + YCoord = max(YCoord, yTopOffset) + canvas.drawLine(xLeftOffset,YCoord,xLeftOffset-5,YCoord) + canvas.drawString(strY, xLeftOffset -30,YCoord +5,font=scaleFont) + YYY += stepY + YCoord -= stepYPixel + + ##draw X Scale + stepX = plotWidth/len(data) + XCoord = xLeftOffset + 0.5*stepX + YCoord = plotHeight + yTopOffset + scaleFont = pid.Font(ttf="tahoma",size=12,bold=0) + labelFont = pid.Font(ttf="tahoma",size=13,bold=0) + for item in data: + itemname, itemvalue = item + canvas.drawLine(XCoord, YCoord,XCoord, YCoord+5, color=pid.black) + canvas.drawString(itemname, XCoord - canvas.stringWidth(itemname,font=labelFont)/2.0,\ + YCoord +20,font=labelFont) + + nValue = len(itemvalue) + catValue = [] + for item2 in itemvalue: + try: + tstrain, tvalue = item2 + except: + tvalue = item2 + if nValue <= 4: + canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5) + else: + catValue.append(tvalue) + if catValue != []: + catMean = gmean(catValue) + catMedian = gmedian(catValue) + lowHinge = gpercentile(catValue, 25) + upHinge = gpercentile(catValue, 75) + Hstep = 1.5*(upHinge - lowHinge) + + outlier = [] + extrem = [] + + upperAdj = None + for item in catValue: + if item >= upHinge + 2*Hstep: + extrem.append(item) + elif item >= upHinge + Hstep: + outlier.append(item) + elif item > upHinge and item < upHinge + Hstep: + if upperAdj == None or item > upperAdj: + upperAdj = item + else: + pass + lowerAdj = None + for item in catValue: + if item <= lowHinge - 2*Hstep: + extrem.append(item) + elif item <= lowHinge - Hstep: + outlier.append(item) + if item < lowHinge and item > lowHinge - Hstep: + if lowerAdj == None or item < lowerAdj: + lowerAdj = item + else: + pass + canvas.drawRect(XCoord-20, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \ + XCoord+20, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll)) + canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll), \ + XCoord+20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll)) + if upperAdj != None: + canvas.drawLine(XCoord, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll), \ + XCoord, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll)) + canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll), \ + XCoord+20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll)) + if lowerAdj != None: + canvas.drawLine(XCoord, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \ + XCoord, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll)) + canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll), \ + XCoord+20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll)) + + outlierFont = pid.Font(ttf="cour",size=12,bold=0) + if outlier != []: + for item in outlier: + yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll) + #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3) + canvas.drawString('o', XCoord-3, yc+5, font=outlierFont, color=pid.orange) + if extrem != []: + for item in extrem: + yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll) + #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3) + canvas.drawString('*', XCoord-3, yc+6, font=outlierFont, color=pid.red) + + canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \ + color=pid.blue,size=3) + #print (catMean, catMedian, cat25per, cat75per) + pass + + XCoord += stepX + + labelFont=pid.Font(ttf="verdana",size=18,bold=0) + canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, \ + YCoord +40, font=labelFont) + canvas.drawString(YLabel,xLeftOffset-40, YCoord-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0,\ + font=labelFont, angle =90) + +def plotSecurity(canvas, text="12345"): + if not text: + return + + plotWidth = canvas.size[0] + plotHeight = canvas.size[1] + if plotHeight<=0 or plotWidth<=0: + return + + bgColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random()) + canvas.drawRect(0,0,plotWidth,plotHeight, edgeColor=bgColor, fillColor=bgColor) + + for i in range(30): + randomColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random()) + scaleFont=pid.Font(ttf="cour",size=random.choice(range(20, 50))) + canvas.drawString(random.choice('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'), + int(random.random()*plotWidth), int(random.random()*plotHeight), font=scaleFont, + color=randomColor, angle=random.choice(range(-45, 50))) + + step = (plotWidth-20)/len(text) + startX = 20 + for item in text: + randomColor = pid.Color(0.6*random.random(),0.6*random.random(), 0.6*random.random()) + scaleFont=pid.Font(ttf="verdana",size=random.choice(range(50, 60)),bold=1) + canvas.drawString(item, startX, plotHeight/2-10, font=scaleFont, + color=randomColor, angle=random.choice(range(-45, 50))) + startX += step + +# parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py) +# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py) +#def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1): +# +# xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset +# +# plotWidth = canvas.size[0] - xLeftOffset - xRightOffset +# plotHeight = canvas.size[1] - yTopOffset - yBottomOffset +# if plotHeight<=0 or plotWidth<=0: +# return +# +# if len(data) < 2: +# return +# +# max_D = max(data) +# min_D = min(data) +# #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong +# if max_D == float('inf') or max_D>webqtlConfig.MAXLRS: +# max_D=webqtlConfig.MAXLRS #maximum LRS value +# +# xLow, xTop, stepX = detScale(min_D, max_D) +# +# #reduce data +# step = ceil((xTop-xLow)/50.0) +# j = xLow +# dataXY = [] +# Count = [] +# while j <= xTop: +# dataXY.append(j) +# Count.append(0) +# j += step +# +# for i, item in enumerate(data): +# if item == float('inf') or item>webqtlConfig.MAXLRS: +# item = webqtlConfig.MAXLRS #maximum LRS value +# j = int((item-xLow)/step) +# Count[j] += 1 +# +# yLow, yTop, stepY=detScale(0,max(Count)) +# +# #draw data +# xScale = plotWidth/(xTop-xLow) +# yScale = plotHeight/(yTop-yLow) +# barWidth = xScale*step +# +# for i, count in enumerate(Count): +# if count: +# xc = (dataXY[i]-xLow)*xScale+xLeftOffset +# yc =-(count-yLow)*yScale+yTopOffset+plotHeight +# canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor) +# +# #draw drawing region +# canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight) +# +# #draw scale +# scaleFont=pid.Font(ttf="cour",size=11,bold=1) +# x=xLow +# for i in range(stepX+1): +# xc=xLeftOffset+(x-xLow)*xScale +# canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor) +# strX = cformat(d=x, rank=0) +# canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont) +# x+= (xTop - xLow)/stepX +# +# y=yLow +# for i in range(stepY+1): +# yc=yTopOffset+plotHeight-(y-yLow)*yScale +# canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor) +# strY = "%d" %y +# canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont) +# y+= (yTop - yLow)/stepY +# +# #draw label +# labelFont=pid.Font(ttf="tahoma",size=17,bold=0) +# if XLabel: +# canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0, +# yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor) +# +# if YLabel: +# canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0, +# font=labelFont,color=labelColor,angle=90) +# +# labelFont=pid.Font(ttf="verdana",size=16,bold=0) +# if title: +# canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0, +# 20,font=labelFont,color=labelColor) +# +#def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, sLabel = None, offset= (80, 20, 40, 100), barSpace = 2, zoom = 1): +# xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset +# plotWidth = canvas.size[0] - xLeftOffset - xRightOffset +# plotHeight = canvas.size[1] - yTopOffset - yBottomOffset +# if plotHeight<=0 or plotWidth<=0: +# return +# +# NNN = len(data) +# if NNN < 2 or NNN != len(label): +# return +# if variance and len(variance)!=NNN: +# variance = [] +# +# Y2 = data[:] +# if variance: +# for i in range(NNN): +# if variance[i]: +# Y2 += [data[i]-variance[i]] +# +# #Y axis +# YLow, YTop, stepY = detScale(min(Y2), max(Y2)) +# YScale = plotHeight/(YTop - YLow) +# +# if YLow < 0 and YTop > 0: +# drawZero = 1 +# else: +# drawZero = 0 +# +# #X axis +# X = range(NNN) +# Xll= 0 +# Xur= NNN-1 +# +# +# if drawZero: +# YZero = yTopOffset+plotHeight-YScale*(0-YLow) +# canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero) +# else: +# YZero = yTopOffset+plotHeight +# #draw data +# spaceWidth = barSpace +# if spaceWidth < 1: +# spaceWidth = 1 +# barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN) +# +# xc= xLeftOffset +# scaleFont=pid.Font(ttf="verdana",size=11,bold=0) +# for i in range(NNN): +# yc = yTopOffset+plotHeight-(data[i]-YLow)*YScale +# canvas.drawRect(xc,YZero,xc+barWidth-1, yc, edgeColor=barColor,fillColor=barColor) +# if variance and variance[i]: +# varlen = variance[i]*YScale +# if yc-varlen < yTopOffset: +# topYd = yTopOffset +# else: +# topYd = yc-varlen +# canvas.drawLine(xc+barWidth/2-2,yc-varlen,xc+barWidth/2+2,yc-varlen,color=pid.red) +# canvas.drawLine(xc+barWidth/2,yc+varlen,xc+barWidth/2,topYd,color=pid.red) +# canvas.drawLine(xc+barWidth/2-2,yc+varlen,xc+barWidth/2+2,yc+varlen,color=pid.red) +# strX = label[i] +# canvas.drawString(strX,xc+barWidth/2.0+2,yTopOffset+plotHeight+2+canvas.stringWidth(strX,font=scaleFont),font=scaleFont,angle=90) +# xc += barWidth + spaceWidth +# +# #draw drawing region +# canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight) +# +# #draw Y scale +# scaleFont=pid.Font(ttf="cour",size=16,bold=1) +# y=YLow +# for i in range(stepY+1): +# yc=yTopOffset+plotHeight-(y-YLow)*YScale +# canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor) +# strY = cformat(d=y, rank=0) +# canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont) +# y+= (YTop - YLow)/stepY +# +# #draw label +# labelFont=pid.Font(ttf="verdana",size=17,bold=0) +# if XLabel: +# canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,yTopOffset+plotHeight+65,font=labelFont,color=labelColor) +# +# if YLabel: +# canvas.drawString(YLabel,xLeftOffset-50, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,font=labelFont,color=labelColor,angle=90) +# +# labelFont=pid.Font(ttf="verdana",size=18,bold=0) +# if title: +# canvas.drawString(title,xLeftOffset,yTopOffset-15,font=labelFont,color=labelColor) +# +# return +# +#def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, axesColor=pid.black, labelColor=pid.black, lineSize="thin", lineColor=pid.grey, idFont="arial", idColor=pid.blue, idSize="14", symbolColor=pid.black, symbolType="circle", filled="yes", symbolSize="tiny", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1, bufferSpace = 15): +# 'displayR : correlation scatter plot, loadings : loading plot' +# +# dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX)) +# +# #get ID font size +# idFontSize = int(idSize) +# +# #If filled is yes, set fill color +# if filled == "yes": +# fillColor = symbolColor +# else: +# fillColor = None +# +# if symbolSize == "large": +# sizeModifier = 7 +# fontModifier = 12 +# elif symbolSize == "medium": +# sizeModifier = 5 +# fontModifier = 8 +# elif symbolSize == "small": +# sizeModifier = 3 +# fontModifier = 3 +# else: +# sizeModifier = 1 +# fontModifier = -1 +# +# if rank == 0: # Pearson correlation +# bufferSpace = 0 +# dataXPrimary = dataX +# dataYPrimary = dataY +# dataXAlt = dataXRanked #Values used just for printing the other corr type to the graph image +# dataYAlt = dataYRanked #Values used just for printing the other corr type to the graph image +# else: # Spearman correlation: Switching Ranked and Unranked X and Y values +# dataXPrimary = dataXRanked +# dataYPrimary = dataYRanked +# dataXAlt = dataX #Values used just for printing the other corr type to the graph image +# dataYAlt = dataY #Values used just for printing the other corr type to the graph image +# +# xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset +# plotWidth = canvas.size[0] - xLeftOffset - xRightOffset +# plotHeight = canvas.size[1] - yTopOffset - yBottomOffset +# if plotHeight<=0 or plotWidth<=0: +# return +# if len(dataXPrimary) < 1 or len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)): +# return +# +# max_X=max(dataXPrimary) +# min_X=min(dataXPrimary) +# max_Y=max(dataYPrimary) +# min_Y=min(dataYPrimary) +# +# #for some reason I forgot why I need to do this +# if loadingPlot: +# min_X = min(-0.1,min_X) +# max_X = max(0.1,max_X) +# min_Y = min(-0.1,min_Y) +# max_Y = max(0.1,max_Y) +# +# xLow, xTop, stepX=detScale(min_X,max_X) +# yLow, yTop, stepY=detScale(min_Y,max_Y) +# xScale = plotWidth/(xTop-xLow) +# yScale = plotHeight/(yTop-yLow) +# +# #draw drawing region +# canvas.drawRect(xLeftOffset-bufferSpace, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace) +# canvas.drawRect(xLeftOffset-bufferSpace+1, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace-1) +# +# #calculate data points +# data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary) +# xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary) +# +# labelFont=pid.Font(ttf=idFont,size=idFontSize,bold=0) +# +# if loadingPlot: +# xZero = -xLow*xScale+xLeftOffset +# yZero = yTopOffset+plotHeight+yLow*yScale +# for point in xCoord: +# canvas.drawLine(xZero,yZero,point[0],point[1],color=pid.red) +# else: +# if connectdot: +# canvas.drawPolygon(xCoord,edgeColor=plotColor,closed=0) +# else: +# pass +# +# symbolFont = pid.Font(ttf="fnt_bs", size=12+fontModifier,bold=0) +# +# for i, item in enumerate(xCoord): +# if dataLabel and dataLabel[i] in specialCases: +# canvas.drawRect(item[0]-3, item[1]-3, item[0]+3, item[1]+3, edgeColor=pid.green) +# #canvas.drawCross(item[0],item[1],color=pid.blue,size=5) +# else: +# if symbolType == "vertRect": +# canvas.drawRect(x1=item[0]-sizeModifier+2,y1=item[1]-sizeModifier-2, x2=item[0]+sizeModifier-1,y2=item[1]+sizeModifier+2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor) +# elif (symbolType == "circle" and filled != "yes"): +# canvas.drawString(":", item[0]-canvas.stringWidth(":",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont) +# elif (symbolType == "circle" and filled == "yes"): +# canvas.drawString("5", item[0]-canvas.stringWidth("5",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont) +# elif symbolType == "horiRect": +# canvas.drawRect(x1=item[0]-sizeModifier-1,y1=item[1]-sizeModifier+3, x2=item[0]+sizeModifier+3,y2=item[1]+sizeModifier-2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor) +# elif (symbolType == "square"): +# canvas.drawRect(x1=item[0]-sizeModifier+1,y1=item[1]-sizeModifier-4, x2=item[0]+sizeModifier+2,y2=item[1]+sizeModifier-3, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor) +# elif (symbolType == "diamond" and filled != "yes"): +# canvas.drawString(",", item[0]-canvas.stringWidth(",",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor) +# elif (symbolType == "diamond" and filled == "yes"): +# canvas.drawString("D", item[0]-canvas.stringWidth("D",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor) +# elif symbolType == "4-star": +# canvas.drawString("l", item[0]-canvas.stringWidth("l",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor) +# elif symbolType == "3-star": +# canvas.drawString("k", item[0]-canvas.stringWidth("k",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor) +# else: +# canvas.drawCross(item[0],item[1]-2,color=symbolColor, size=sizeModifier+2) +# +# if showLabel and dataLabel: +# if (symbolType == "vertRect" or symbolType == "diamond"): +# labelGap = 15 +# elif (symbolType == "4-star" or symbolType == "3-star"): +# labelGap = 12 +# else: +# labelGap = 11 +# canvas.drawString(dataLabel[i], item[0]- canvas.stringWidth(dataLabel[i], +# font=labelFont)/2 + 1, item[1]+(labelGap+sizeModifier+(idFontSize-12)), font=labelFont, color=idColor) +# +# #draw scale +# scaleFont=pid.Font(ttf="cour",size=16,bold=1) +# +# +# x=xLow +# for i in range(stepX+1): +# xc=xLeftOffset+(x-xLow)*xScale +# if ((x == 0) & (rank == 1)): +# pass +# else: +# canvas.drawLine(xc,yTopOffset+plotHeight + bufferSpace,xc,yTopOffset+plotHeight+5 + bufferSpace, color=axesColor) +# strX = cformat(d=x, rank=rank) +# if ((strX == "0") & (rank == 1)): +# pass +# else: +# canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+20 + bufferSpace,font=scaleFont) +# x+= (xTop - xLow)/stepX +# +# y=yLow +# for i in range(stepY+1): +# yc=yTopOffset+plotHeight-(y-yLow)*yScale +# if ((y == 0) & (rank == 1)): +# pass +# else: +# canvas.drawLine(xLeftOffset - bufferSpace,yc,xLeftOffset-5 - bufferSpace,yc, color=axesColor) +# strY = cformat(d=y, rank=rank) +# if ((strY == "0") & (rank == 1)): +# pass +# else: +# canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)- 10 - bufferSpace,yc+4,font=scaleFont) +# y+= (yTop - yLow)/stepY +# +# #draw label +# +# labelFont=pid.Font(ttf="verdana",size=canvas.size[0]/45,bold=0) +# titleFont=pid.Font(ttf="verdana",size=canvas.size[0]/40,bold=0) +# +# if (rank == 1 and not title): +# canvas.drawString("Spearman Rank Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Spearman Rank Correlation",font=titleFont))/2.0, +# 25,font=titleFont,color=labelColor) +# elif (rank == 0 and not title): +# canvas.drawString("Pearson Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Pearson Correlation",font=titleFont))/2.0, +# 25,font=titleFont,color=labelColor) +# +# if XLabel: +# canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0, +# yTopOffset+plotHeight+yBottomOffset-25,font=labelFont,color=labelColor) +# +# if YLabel: +# canvas.drawString(YLabel, xLeftOffset-65, yTopOffset+plotHeight- (plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0, +# font=labelFont,color=labelColor,angle=90) +# +# labelFont=pid.Font(ttf="verdana",size=20,bold=0) +# if title: +# canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0, +# 20,font=labelFont,color=labelColor) +# +# if fitcurve: +# import sys +# sys.argv = [ "mod_python" ] +# #from numarray import linear_algebra as la +# #from numarray import ones, array, dot, swapaxes +# fitYY = array(dataYPrimary) +# fitXX = array([ones(len(dataXPrimary)),dataXPrimary]) +# AA = dot(fitXX,swapaxes(fitXX,0,1)) +# BB = dot(fitXX,fitYY) +# bb = la.linear_least_squares(AA,BB)[0] +# +# xc1 = xLeftOffset +# yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale +# if yc1 > yTopOffset+plotHeight: +# yc1 = yTopOffset+plotHeight +# xc1 = (yLow-bb[0])/bb[1] +# xc1=(xc1-xLow)*xScale+xLeftOffset +# elif yc1 < yTopOffset: +# yc1 = yTopOffset +# xc1 = (yTop-bb[0])/bb[1] +# xc1=(xc1-xLow)*xScale+xLeftOffset +# else: +# pass +# +# xc2 = xLeftOffset + plotWidth +# yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale +# if yc2 > yTopOffset+plotHeight: +# yc2 = yTopOffset+plotHeight +# xc2 = (yLow-bb[0])/bb[1] +# xc2=(xc2-xLow)*xScale+xLeftOffset +# elif yc2 < yTopOffset: +# yc2 = yTopOffset +# xc2 = (yTop-bb[0])/bb[1] +# xc2=(xc2-xLow)*xScale+xLeftOffset +# else: +# pass +# +# canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace,xc2,yc2,color=lineColor) +# if lineSize == "medium": +# canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor) +# if lineSize == "thick": +# canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor) +# canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace-1,xc2,yc2-1,color=lineColor) +# +# +# if displayR: +# labelFont=pid.Font(ttf="trebuc",size=canvas.size[0]/60,bold=0) +# NNN = len(dataX) +# corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0] +# +# if NNN < 3: +# corrPValue = 1.0 +# else: +# if abs(corr) >= 1.0: +# corrPValue = 0.0 +# else: +# ZValue = 0.5*log((1.0+corr)/(1.0-corr)) +# ZValue = ZValue*sqrt(NNN-3) +# corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue))) +# +# NStr = "N = %d" % NNN +# strLenN = canvas.stringWidth(NStr,font=labelFont) +# +# if rank == 1: +# if corrPValue < 0.0000000000000001: +# corrStr = "Rho = %1.3f P < 1.00 E-16" % (corr) +# else: +# corrStr = "Rho = %1.3f P = %3.2E" % (corr, corrPValue) +# else: +# if corrPValue < 0.0000000000000001: +# corrStr = "r = %1.3f P < 1.00 E-16" % (corr) +# else: +# corrStr = "r = %1.3f P = %3.2E" % (corr, corrPValue) +# strLen = canvas.stringWidth(corrStr,font=labelFont) +# +# canvas.drawString(NStr,xLeftOffset,yTopOffset-10,font=labelFont,color=labelColor) +# canvas.drawString(corrStr,xLeftOffset+plotWidth-strLen,yTopOffset-10,font=labelFont,color=labelColor) +# +# return xCoord + +def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black", axesColor="black", labelColor="black", symbolColor="red", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1): + 'displayR : correlation scatter plot, loadings : loading plot' + + dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX)) + + # Switching Ranked and Unranked X and Y values if a Spearman Rank Correlation + if rank == 0: + dataXPrimary = dataX + dataYPrimary = dataY + dataXAlt = dataXRanked + dataYAlt = dataYRanked + + else: + dataXPrimary = dataXRanked + dataYPrimary = dataYRanked + dataXAlt = dataX + dataYAlt = dataY + + + + xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset + plotWidth = drawSpace.attributes['width'] - xLeftOffset - xRightOffset + plotHeight = drawSpace.attributes['height'] - yTopOffset - yBottomOffset + if plotHeight<=0 or plotWidth<=0: + return + if len(dataXPrimary) < 1 or len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)): + return + + max_X=max(dataXPrimary) + min_X=min(dataXPrimary) + max_Y=max(dataYPrimary) + min_Y=min(dataYPrimary) + + #for some reason I forgot why I need to do this + if loadingPlot: + min_X = min(-0.1,min_X) + max_X = max(0.1,max_X) + min_Y = min(-0.1,min_Y) + max_Y = max(0.1,max_Y) + + xLow, xTop, stepX=detScale(min_X,max_X) + yLow, yTop, stepY=detScale(min_Y,max_Y) + xScale = plotWidth/(xTop-xLow) + yScale = plotHeight/(yTop-yLow) + + #draw drawing region + r = svg.rect(xLeftOffset, yTopOffset, plotWidth, plotHeight, 'none', axesColor, 1) + drawSpace.addElement(r) + + #calculate data points + data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary) + xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary) + labelFontF = "verdana" + labelFontS = 11 + + if loadingPlot: + xZero = -xLow*xScale+xLeftOffset + yZero = yTopOffset+plotHeight+yLow*yScale + for point in xCoord: + drawSpace.addElement(svg.line(xZero,yZero,point[0],point[1], "red", 1)) + else: + if connectdot: + pass + #drawSpace.drawPolygon(xCoord,edgeColor=plotColor,closed=0) + else: + pass + + for i, item in enumerate(xCoord): + if dataLabel and dataLabel[i] in specialCases: + drawSpace.addElement(svg.rect(item[0]-3, item[1]-3, 6, 6, "none", "green", 0.5)) + #drawSpace.drawCross(item[0],item[1],color=pid.blue,size=5) + else: + drawSpace.addElement(svg.line(item[0],item[1]+5,item[0],item[1]-5,symbolColor,1)) + drawSpace.addElement(svg.line(item[0]+5,item[1],item[0]-5,item[1],symbolColor,1)) + if showLabel and dataLabel: + pass + drawSpace.addElement(svg.text(item[0], item[1]+14, dataLabel[i], labelFontS, + labelFontF, text_anchor="middle", style="stroke:blue;stroke-width:0.5;")) + #canvas.drawString(, item[0]- canvas.stringWidth(dataLabel[i], + # font=labelFont)/2, item[1]+14, font=labelFont, color=pid.blue) + + #draw scale + #scaleFont=pid.Font(ttf="cour",size=14,bold=1) + x=xLow + for i in range(stepX+1): + xc=xLeftOffset+(x-xLow)*xScale + drawSpace.addElement(svg.line(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, axesColor, 1)) + strX = cformat(d=x, rank=rank) + drawSpace.addElement(svg.text(xc,yTopOffset+plotHeight+20,strX,13, "courier", text_anchor="middle")) + x+= (xTop - xLow)/stepX + + y=yLow + for i in range(stepY+1): + yc=yTopOffset+plotHeight-(y-yLow)*yScale + drawSpace.addElement(svg.line(xLeftOffset,yc,xLeftOffset-5,yc, axesColor, 1)) + strY = cformat(d=y, rank=rank) + drawSpace.addElement(svg.text(xLeftOffset-10,yc+5,strY,13, "courier", text_anchor="end")) + y+= (yTop - yLow)/stepY + + #draw label + labelFontF = "verdana" + labelFontS = 17 + if XLabel: + drawSpace.addElement(svg.text(xLeftOffset+plotWidth/2.0, + yTopOffset+plotHeight+yBottomOffset-10,XLabel, + labelFontS, labelFontF, text_anchor="middle")) + + if YLabel: + drawSpace.addElement(svg.text(xLeftOffset-50, + yTopOffset+plotHeight/2,YLabel, + labelFontS, labelFontF, text_anchor="middle", style="writing-mode:tb-rl", transform="rotate(270 %d %d)" % (xLeftOffset-50, yTopOffset+plotHeight/2))) + #drawSpace.drawString(YLabel, xLeftOffset-50, yTopOffset+plotHeight- (plotHeight-drawSpace.stringWidth(YLabel,font=labelFont))/2.0, + # font=labelFont,color=labelColor,angle=90) + + + if fitcurve: + sys.argv = [ "mod_python" ] + #from numarray import linear_algebra as la + #from numarray import ones, array, dot, swapaxes + fitYY = array(dataYPrimary) + fitXX = array([ones(len(dataXPrimary)),dataXPrimary]) + AA = dot(fitXX,swapaxes(fitXX,0,1)) + BB = dot(fitXX,fitYY) + bb = la.linear_least_squares(AA,BB)[0] + + xc1 = xLeftOffset + yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale + if yc1 > yTopOffset+plotHeight: + yc1 = yTopOffset+plotHeight + xc1 = (yLow-bb[0])/bb[1] + xc1=(xc1-xLow)*xScale+xLeftOffset + elif yc1 < yTopOffset: + yc1 = yTopOffset + xc1 = (yTop-bb[0])/bb[1] + xc1=(xc1-xLow)*xScale+xLeftOffset + else: + pass + + xc2 = xLeftOffset + plotWidth + yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale + if yc2 > yTopOffset+plotHeight: + yc2 = yTopOffset+plotHeight + xc2 = (yLow-bb[0])/bb[1] + xc2=(xc2-xLow)*xScale+xLeftOffset + elif yc2 < yTopOffset: + yc2 = yTopOffset + xc2 = (yTop-bb[0])/bb[1] + xc2=(xc2-xLow)*xScale+xLeftOffset + else: + pass + + drawSpace.addElement(svg.line(xc1,yc1,xc2,yc2,"green", 1)) + + if displayR: + labelFontF = "trebuc" + labelFontS = 14 + NNN = len(dataX) + + corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0] + + if NNN < 3: + corrPValue = 1.0 + else: + if abs(corr) >= 1.0: + corrPValue = 0.0 + else: + ZValue = 0.5*log((1.0+corr)/(1.0-corr)) + ZValue = ZValue*sqrt(NNN-3) + corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue))) + + NStr = "N of Cases=%d" % NNN + + if rank == 1: + corrStr = "Spearman's r=%1.3f P=%3.2E" % (corr, corrPValue) + else: + corrStr = "Pearson's r=%1.3f P=%3.2E" % (corr, corrPValue) + + drawSpace.addElement(svg.text(xLeftOffset,yTopOffset-10,NStr, + labelFontS, labelFontF, text_anchor="start")) + drawSpace.addElement(svg.text(xLeftOffset+plotWidth,yTopOffset-25,corrStr, + labelFontS, labelFontF, text_anchor="end")) + """ + """ + return + + +# This function determines the scale of the plot +def detScaleOld(min,max): + if min>=max: + return None + elif min == -1.0 and max == 1.0: + return [-1.2,1.2,12] + else: + a=max-min + b=floor(log10(a)) + c=pow(10.0,b) + if a < c*5.0: + c/=2.0 + #print a,b,c + low=c*floor(min/c) + high=c*ceil(max/c) + return [low,high,round((high-low)/c)] + +def detScale(min=0,max=0,bufferSpace=3): + + if min>=max: + return None + elif min == -1.0 and max == 1.0: + return [-1.2,1.2,12] + else: + a=max-min + if max != 0: + max += 0.1*a + if min != 0: + if min > 0 and min < 0.1*a: + min = 0.0 + else: + min -= 0.1*a + a=max-min + b=floor(log10(a)) + c=pow(10.0,b) + low=c*floor(min/c) + high=c*ceil(max/c) + n = round((high-low)/c) + div = 2.0 + while n < 5 or n > 15: + if n < 5: + c /= div + else: + c *= div + if div == 2.0: + div =5.0 + else: + div =2.0 + low=c*floor(min/c) + high=c*ceil(max/c) + n = round((high-low)/c) + + return [low,high,n] + + + +def colorSpectrumOld(n): + if n == 1: + return [pid.Color(1,0,0)] + elif n == 2: + return [pid.Color(1,0,0),pid.Color(0,0,1)] + elif n == 3: + return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)] + else: + step = 2.0/(n-1) + red = 1.0 + green = 0.0 + blue = 0.0 + colors = [pid.Color(red,green,blue)] + i = 1 + greenpeak = 0 + while i < n: + if red >= step: + red -= step + green += step + if green >= 1.0: + greenpeak = 1 + blue += green -1.0 + green = 1.0 + else: + red = 0.0 + if greenpeak: + green -= step + blue += step + else: + green += step + if green >= 1.0: + greenpeak = 1 + blue += green -1.0 + green = 2.0 -green + elif green < 0.0: + green = 0.0 + else: + pass + colors.append(pid.Color(red,green,blue)) + i += 1 + return colors + + + + +def bluefunc(x): + return 1.0 / (1.0 + exp(-10*(x-0.6))) + + +def redfunc(x): + return 1.0 / (1.0 + exp(10*(x-0.5))) + +def greenfunc(x): + return 1 - pow(redfunc(x+0.2),2) - bluefunc(x-0.3) + +def colorSpectrum(n=100): + multiple = 10 + if n == 1: + return [pid.Color(1,0,0)] + elif n == 2: + return [pid.Color(1,0,0),pid.Color(0,0,1)] + elif n == 3: + return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)] + N = n*multiple + out = [None]*N; + for i in range(N): + x = float(i)/N + out[i] = pid.Color(redfunc(x), greenfunc(x), bluefunc(x)); + out2 = [out[0]] + step = N/float(n-1) + j = 0 + for i in range(n-2): + j += step + out2.append(out[int(j)]) + out2.append(out[-1]) + return out2 + + +def colorSpectrumSVG(n=100): + multiple = 10 + if n == 1: + return ["rgb(255,0,0)"] + elif n == 2: + return ["rgb(255,0,0)","rgb(0,0,255)"] + elif n == 3: + return ["rgb(255,0,0)","rgb(0,255,0)","rgb(0,0,255)"] + N = n*multiple + out = [None]*N; + for i in range(N): + x = float(i)/N + out[i] = "rgb(%d, %d, %d)" % (redfunc(x)*255, greenfunc(x)*255, bluefunc(x)*255); + out2 = [out[0]] + step = N/float(n-1) + j = 0 + for i in range(n-2): + j += step + out2.append(out[int(j)]) + out2.append(out[-1]) + return out2 + + +def BWSpectrum(n=100): + multiple = 10 + if n == 1: + return [pid.Color(0,0,0)] + elif n == 2: + return [pid.Color(0,0,0),pid.Color(1,1,1)] + elif n == 3: + return [pid.Color(0,0,0),pid.Color(0.5,0.5,0.5),pid.Color(1,1,1)] + + step = 1.0/n + x = 0.0 + out = [] + for i in range(n): + out.append(pid.Color(x,x,x)); + x += step + return out + + +def _test(): + import doctest + doctest.testmod() + + +if __name__=="__main__": + _test() |