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authorSam Ockman2012-06-02 04:43:31 -0400
committerSam Ockman2012-06-02 04:43:31 -0400
commit93fdf06d57770c985e0ca8169977c210a891e262 (patch)
treed6007a2838a25ac0e5e23c4663ea81c99dec6a2f /wqflask/utility
parentf7c2c6ff903f835ddef2daffa368ae1aa26e136a (diff)
downloadgenenetwork2-93fdf06d57770c985e0ca8169977c210a891e262.tar.gz
Coming along in trying to get trait page working
Diffstat (limited to 'wqflask/utility')
-rwxr-xr-xwqflask/utility/Plot.py334
1 files changed, 167 insertions, 167 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 2401c85c..e00b8e9e 100755
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -24,7 +24,7 @@
#
# Last updated by GeneNetwork Core Team 2010/10/20
-import piddle as pid
+#import piddle as pid
from math import *
import random
import sys, os
@@ -41,7 +41,7 @@ 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:
@@ -51,29 +51,29 @@ def cformat(d, rank=0):
break
else:
strD = strD[:-1]
-
+
else:
- strD = strD.split(".")[0]
+ 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 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):
@@ -85,15 +85,15 @@ def gammln(xx):
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]
@@ -109,7 +109,7 @@ def gser(a,x):
gamser=sum*exp(-x+a*log(x)-gln)
return [gamser,gln]
return None
-
+
def gcf(a,x):
ITMAX=100
EPS=3.0e-7
@@ -119,7 +119,7 @@ def gcf(a,x):
b0=0.0
a0=1.0
gln=gammln(a)
-
+
a1=x
for n in range(1,ITMAX+1):
an=n+0.0
@@ -137,7 +137,7 @@ def gcf(a,x):
return [gammcf,gln]
gold=g
return None
-
+
def gammp(a,x):
if x<0.0 or a<=0.0:
return None
@@ -155,7 +155,7 @@ def U(n):
m.append(a)
m.append(x)
return m
-
+
def erf(x):
if x<0.0:
return -gammp(0.5,x*x)
@@ -170,7 +170,7 @@ def erfcc(x):
return ans
else:
return 2.0-ans
-
+
def calMeanVar(data):
n=len(data)
if n<2:
@@ -187,7 +187,7 @@ def calMeanVar(data):
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]
@@ -227,7 +227,7 @@ def inverseCumul(p):
return None
if p>0 and p < 1:
- e = 0.5 * erfcc(-x/sqrt(2)) - p
+ 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
@@ -252,7 +252,7 @@ def gmedian(lst2):
return (lst[N/2]+lst[(N-2)/2])/2.0
else:
return lst[(N-1)/2]
-
+
def gpercentile(lst2, np):
lst = lst2[:]
N = len(lst)
@@ -269,21 +269,21 @@ def gpercentile(lst2, np):
return lst[N-1]
else:
return lst[k-1] + d*(lst[k] - lst[k-1])
-
+
def findOutliers(vals):
-
+
valsOnly = []
dataXZ = vals[:]
for i in range(len(dataXZ)):
valsOnly.append(dataXZ[i][1])
-
- data = [('', valsOnly[:])]
-
+
+ data = [('', valsOnly[:])]
+
for item in data:
itemvalue = item[1]
nValue = len(itemvalue)
catValue = []
-
+
for item2 in itemvalue:
try:
tstrain, tvalue = item2
@@ -293,18 +293,18 @@ def findOutliers(vals):
continue
else:
catValue.append(tvalue)
-
+
if catValue != []:
lowHinge = gpercentile(catValue, 25)
upHinge = gpercentile(catValue, 75)
Hstep = 1.5*(upHinge - lowHinge)
-
+
outlier = []
extreme = []
-
+
upperBound = upHinge + Hstep
lowerBound = lowHinge - Hstep
-
+
for item in catValue:
if item >= upHinge + 2*Hstep:
extreme.append(item)
@@ -312,7 +312,7 @@ def findOutliers(vals):
outlier.append(item)
else:
pass
-
+
for item in catValue:
if item <= lowHinge - 2*Hstep:
extreme.append(item)
@@ -323,10 +323,10 @@ def findOutliers(vals):
else:
upperBound = 1000
lowerBound = -1000
-
+
return upperBound, lowerBound
-
-
+
+
def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabel="Value"):
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -338,8 +338,8 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe
iValues.append(item2[1])
except:
iValues.append(item2)
-
- #draw frame
+
+ #draw frame
max_Y = max(iValues)
min_Y = min(iValues)
scaleY = detScale(min_Y, max_Y)
@@ -349,7 +349,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe
stepY = (Yur - Yll)/nStep
stepYPixel = plotHeight/(nStep)
canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset)
-
+
##draw Y Scale
YYY = Yll
YCoord = plotHeight + yTopOffset
@@ -361,7 +361,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe
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
@@ -373,7 +373,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe
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:
@@ -391,10 +391,10 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe
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:
@@ -431,7 +431,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe
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:
@@ -443,14 +443,14 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe
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)
@@ -465,48 +465,48 @@ def plotSecurity(canvas, text="12345"):
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,
+ 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,
+ 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)
+# 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
@@ -515,27 +515,27 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
while j <= xTop:
dataXY.append(j)
Count.append(0)
- j += step
-
+ 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
-
+ 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)
@@ -548,7 +548,7 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
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
@@ -556,13 +556,13 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
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)
@@ -578,34 +578,34 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor
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
+ Xll= 0
Xur= NNN-1
-
-
+
+
if drawZero:
YZero = yTopOffset+plotHeight-YScale*(0-YLow)
canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero)
@@ -616,9 +616,9 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor
if spaceWidth < 1:
spaceWidth = 1
barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN)
-
+
xc= xLeftOffset
- scaleFont=pid.Font(ttf="verdana",size=11,bold=0)
+ 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)
@@ -633,13 +633,13 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor
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
-
+ 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)
+ scaleFont=pid.Font(ttf="cour",size=16,bold=1)
y=YLow
for i in range(stepY+1):
yc=yTopOffset+plotHeight-(y-YLow)*YScale
@@ -647,35 +647,35 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, 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)
-
+ idFontSize = int(idSize)
+
#If filled is yes, set fill color
if filled == "yes":
fillColor = symbolColor
else:
- fillColor = None
-
+ fillColor = None
+
if symbolSize == "large":
sizeModifier = 7
fontModifier = 12
@@ -687,8 +687,8 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
fontModifier = 3
else:
sizeModifier = 1
- fontModifier = -1
-
+ fontModifier = -1
+
if rank == 0: # Pearson correlation
bufferSpace = 0
dataXPrimary = dataX
@@ -700,7 +700,7 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
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
@@ -708,29 +708,29 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
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
+ #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)
@@ -767,12 +767,12 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
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)
+ 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)
+ 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.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:
@@ -784,10 +784,10 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
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):
@@ -795,14 +795,14 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
if ((x == 0) & (rank == 1)):
pass
else:
- canvas.drawLine(xc,yTopOffset+plotHeight + bufferSpace,xc,yTopOffset+plotHeight+5 + bufferSpace, color=axesColor)
+ 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
@@ -816,23 +816,23 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
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)
@@ -841,7 +841,7 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
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" ]
@@ -852,9 +852,9 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
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
+ yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale
if yc1 > yTopOffset+plotHeight:
yc1 = yTopOffset+plotHeight
xc1 = (yLow-bb[0])/bb[1]
@@ -865,8 +865,8 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
xc1=(xc1-xLow)*xScale+xLeftOffset
else:
pass
-
- xc2 = xLeftOffset + plotWidth
+
+ xc2 = xLeftOffset + plotWidth
yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
if yc2 > yTopOffset+plotHeight:
yc2 = yTopOffset+plotHeight
@@ -885,8 +885,8 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
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)
@@ -901,7 +901,7 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
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)
@@ -924,24 +924,24 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax
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
+
+ # 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:
+ 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
@@ -949,34 +949,34 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black"
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
+
+ #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
@@ -988,7 +988,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black"
#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))
@@ -998,11 +998,11 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black"
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,
+ 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
@@ -1012,7 +1012,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black"
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
@@ -1020,7 +1020,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black"
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
@@ -1028,7 +1028,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black"
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,
@@ -1046,9 +1046,9 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black"
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
+ yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale
if yc1 > yTopOffset+plotHeight:
yc1 = yTopOffset+plotHeight
xc1 = (yLow-bb[0])/bb[1]
@@ -1059,8 +1059,8 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black"
xc1=(xc1-xLow)*xScale+xLeftOffset
else:
pass
-
- xc2 = xLeftOffset + plotWidth
+
+ xc2 = xLeftOffset + plotWidth
yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
if yc2 > yTopOffset+plotHeight:
yc2 = yTopOffset+plotHeight
@@ -1074,8 +1074,8 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black"
pass
drawSpace.addElement(svg.line(xc1,yc1,xc2,yc2,"green", 1))
-
- if displayR:
+
+ if displayR:
labelFontF = "trebuc"
labelFontS = 14
NNN = len(dataX)
@@ -1091,24 +1091,24 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black"
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
+# This function determines the scale of the plot
def detScaleOld(min,max):
if min>=max:
return None
@@ -1205,8 +1205,8 @@ def colorSpectrumOld(n):
colors.append(pid.Color(red,green,blue))
i += 1
return colors
-
-
+
+
def bluefunc(x):
@@ -1273,7 +1273,7 @@ def BWSpectrum(n=100):
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 = []