# 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
from __future__ import print_function
import piddle as pid
from pprint import pformat as pf
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("..") Never in a running webserver
from basicStatistics import corestats
import svg
import webqtlUtil
from base import webqtlConfig
import utility.logger
logger = utility.logger.getLogger(__name__ )
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)
"""
logger.debug("xerxes vals is:", pf(vals))
if vals:
#logger.debug("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
logger.debug(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
#ZS: Used to determine number of bins for permutation output
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(int(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(int(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()
