# 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
import webqtlUtil
import corestats
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 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)
"""
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
return upper_bound, lower_bound
# 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)
# 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):
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 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 _test():
import doctest
doctest.testmod()
if __name__=="__main__":
_test()
