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-rw-r--r--wqflask/utility/Plot.py989
1 files changed, 3 insertions, 986 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index d60e2bb2..529cd117 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -36,11 +36,9 @@ 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
+import corestats
from base import webqtlConfig
import utility.logger
@@ -83,202 +81,6 @@ def frange(start, end=None, inc=1.0):
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
@@ -315,165 +117,6 @@ def find_outliers(vals):
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):
@@ -561,542 +204,6 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
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:
@@ -1114,7 +221,7 @@ def detScaleOld(min,max):
high=c*ceil(max/c)
return [low,high,round((high-low)/c)]
-def detScale(min=0,max=0,bufferSpace=3):
+def detScale(min=0,max=0):
if min>=max:
return None
@@ -1151,57 +258,9 @@ def detScale(min=0,max=0,bufferSpace=3):
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)))
@@ -1230,52 +289,10 @@ def colorSpectrum(n=100):
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()
+ _test() \ No newline at end of file
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 01:46:29 +0000