diff options
Diffstat (limited to 'web/webqtl/utility')
| -rwxr-xr-x | web/webqtl/utility/AJAX_table.py | 153 | ||||
| -rwxr-xr-x | web/webqtl/utility/Plot.py | 1283 | ||||
| -rwxr-xr-x | web/webqtl/utility/TDCell.py | 42 | ||||
| -rwxr-xr-x | web/webqtl/utility/THCell.py | 44 | ||||
| -rwxr-xr-x | web/webqtl/utility/__init__.py | 0 | ||||
| -rwxr-xr-x | web/webqtl/utility/svg.py | 1069 | ||||
| -rwxr-xr-x | web/webqtl/utility/webqtlUtil.py | 977 |
7 files changed, 0 insertions, 3568 deletions
diff --git a/web/webqtl/utility/AJAX_table.py b/web/webqtl/utility/AJAX_table.py deleted file mode 100755 index 963a530e..00000000 --- a/web/webqtl/utility/AJAX_table.py +++ /dev/null @@ -1,153 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -import cPickle -import os -import MySQLdb -import time -import pyXLWriter as xl - -from htmlgen import HTMLgen2 as HT - -from base import webqtlConfig -from THCell import THCell -from TDCell import TDCell -import webqtlUtil - - -class AJAX_table: - def __init__(self, fd): - file = fd.formdata.getfirst("file", "") - sort = fd.formdata.getfirst("sort", "") - order = fd.formdata.getfirst("order", "up") - cmd = fd.formdata.getfirst("cmd", "") - tableID = fd.formdata.getfirst("tableID", "") - addIndex = fd.formdata.getfirst("addIndex", "1") - hiddenColumnsString = fd.formdata.getfirst("hiddenColumns", "") - hiddenColumns = hiddenColumnsString.split(',') - - try: - fp = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'rb') - tblobj = cPickle.load(fp) - fp.close() - - if cmd == 'addCorr': - dbId = int(fd.formdata.getfirst("db")) - dbFullName = fd.formdata.getfirst("dbname") - trait = fd.formdata.getfirst("trait") - form = fd.formdata.getfirst("form") - ids = fd.formdata.getfirst("ids") - vals = fd.formdata.getfirst("vals") - ids = eval(ids) - nnCorr = len(ids) - vals = eval(vals) - - workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+file)) - worksheet = workbook.add_worksheet() - - con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) - cursor = con.cursor() - - cursor.execute("Select name, ShortName from ProbeSetFreeze where Id = %s", dbId) - dbName, dbShortName = cursor.fetchone() - - tblobj['header'][0].append( - THCell(HT.TD(dbShortName, Class="fs11 ffl b1 cw cbrb"), - text="%s" % dbShortName, idx=tblobj['header'][0][-1].idx + 1), - ) - - headingStyle = workbook.add_format(align = 'center', bold = 1, border = 1, size=13, fg_color = 0x1E, color="white") - for i, item in enumerate(tblobj['header'][0]): - if (i > 0): - worksheet.write([8, i-1], item.text, headingStyle) - worksheet.set_column([i-1, i-1], 2*len(item.text)) - - for i, row in enumerate(tblobj['body']): - ProbeSetId = row[1].text - #XZ, 03/02/2009: Xiaodong changed Data to ProbeSetData - cursor.execute(""" - Select ProbeSetData.StrainId, ProbeSetData.Value - From ProbeSetData, ProbeSetXRef, ProbeSet - where ProbeSetXRef.ProbeSetFreezeId = %d AND - ProbeSetXRef.DataId = ProbeSetData.Id AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSet.Name = '%s' - """ % (dbId, ProbeSetId)) - results = cursor.fetchall() - vdict = {} - for item in results: - vdict[item[0]] = item[1] - newvals = [] - for id in ids: - if vdict.has_key(id): - newvals.append(vdict[id]) - else: - newvals.append(None) - corr,nOverlap= webqtlUtil.calCorrelation(newvals,vals,nnCorr) - repr = '%0.4f' % corr - row.append( - TDCell(HT.TD(HT.Href(text=repr, url="javascript:showCorrPlotThird('%s', '%s', '%s')" % (form, dbName, ProbeSetId), Class="fs11 fwn ffl"), " / ", nOverlap, Class="fs11 fwn ffl b1 c222", align="middle"),repr,abs(corr)) - ) - - last_row=0 - for j, item in enumerate(tblobj['body'][i]): - if (j > 0): - worksheet.write([9+i, j-1], item.text) - last_row = 9+i - last_row += 1 - - titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray") - ##Write title Info - # Modified by Hongqiang Li - worksheet.write([0, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle) - worksheet.write([1, 0], "Trait : %s" % trait, titleStyle) - worksheet.write([2, 0], "Database : %s" % dbFullName, titleStyle) - worksheet.write([3, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle) - worksheet.write([4, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle) - worksheet.write([5, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle) - #Write footer info - worksheet.write([1 + last_row, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)", titleStyle) - worksheet.write([2 + last_row, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle) - - cursor.close() - workbook.close() - - objfile = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'wb') - cPickle.dump(tblobj, objfile) - objfile.close() - else: - pass - - self.value = str(webqtlUtil.genTableObj(tblobj=tblobj, file=file, sortby=(sort, order), tableID = tableID, addIndex = addIndex, hiddenColumns = hiddenColumns)) - - except: - self.value = "<span class='fs16 fwb cr ffl'>The table is no longer available on this server</span>" - - def __str__(self): - return self.value - - def write(self): - return str(self) diff --git a/web/webqtl/utility/Plot.py b/web/webqtl/utility/Plot.py deleted file mode 100755 index 2401c85c..00000000 --- a/web/webqtl/utility/Plot.py +++ /dev/null @@ -1,1283 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -import piddle as pid -from math import * -import random -import sys, os -from numarray import linear_algebra as la -from numarray import ones, array, dot, swapaxes - -import reaper - -import svg -import webqtlUtil -from base import webqtlConfig - - -def cformat(d, rank=0): - 'custom string format' - strD = "%2.6f" % d - - if rank == 0: - while strD[-1] in ('0','.'): - if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4: - break - elif strD[-1] == '.': - strD = strD[:-1] - break - else: - strD = strD[:-1] - - else: - strD = strD.split(".")[0] - - if strD == '-0.0': - strD = '0.0' - return strD - -def frange(start, end=None, inc=1.0): - "A faster range-like function that does accept float increments..." - if end == None: - end = start + 0.0 - start = 0.0 - else: - start += 0.0 # force it to be a float - count = int((end - start) / inc) - if start + count * inc != end: - # Need to adjust the count. AFAICT, it always comes up one short. - count += 1 - L = [start] * count - for i in xrange(1, count): - L[i] = start + i * inc - return L - - -def gammln(xx): - cof=[76.18009173,-86.50532033,24.01409822,-1.231739516,0.120858003e-2,-0.536382e-5] - x=xx-1.0 - tmp=x+5.5 - tmp -=(x+0.5)*log(tmp) - ser=1.0 - for item in cof: - x+=1.0 - ser+=item/x - - return -tmp+log(2.50662827465*ser) - - -def gser(a,x): - gln=gammln(a) - ITMAX=100 - EPS=3.0e-7 - - if x<=0.0: - gamser=0.0 - return [gamser,gln] - else: - ap=a - sum=1.0/a - dele=sum - for i in range(1,ITMAX+1): - ap+=1.0 - dele*=x/ap - sum+=dele - if abs(dele)<abs(sum)*EPS: - gamser=sum*exp(-x+a*log(x)-gln) - return [gamser,gln] - return None - -def gcf(a,x): - ITMAX=100 - EPS=3.0e-7 - gold=0.0 - fac=1 - b1=1.0 - b0=0.0 - a0=1.0 - gln=gammln(a) - - a1=x - for n in range(1,ITMAX+1): - an=n+0.0 - ana=an-a - a0=(a1+a0*ana)*fac - b0=(b1+b0*ana)*fac - anf=an*fac - a1=x*a0+anf*a1 - b1=x*b0+anf*b1 - if (a1): - fac=1.0/a1 - g=b1*fac - if abs((g-gold)/g)<EPS: - gammcf=exp(-x+a*log(x)-gln)*g - return [gammcf,gln] - gold=g - return None - -def gammp(a,x): - if x<0.0 or a<=0.0: - return None - if x<(a+1.0): - a=gser(a,x)[0] - return a - else: - a=gcf(a,x)[0] - return 1.0-a -def U(n): - x=pow(0.5,1.0/n) - m=[1-x] - for i in range(2,n): - a=(i-0.3175)/(n+0.365) - m.append(a) - m.append(x) - return m - -def erf(x): - if x<0.0: - return -gammp(0.5,x*x) - else: - return gammp(0.5,x*x) - -def erfcc(x): - z=abs(x) - t=1.0/(1.0+0.5*z) - ans=t*exp(-z*z-1.26551223+t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+t*(0.27886807+t*(-1.13520398+t*(1.48851587+t*(-0.82215223+t*0.17087277))))))))) - if x>=0.0: - return ans - else: - return 2.0-ans - -def calMeanVar(data): - n=len(data) - if n<2: - return None - else: - sum=reduce(lambda x,y:x+y,data,0.0) - mean=sum/n - z=data[:] - for i in range(n): - z[i]=z[i]-mean - variance=reduce(lambda x,y:x+y*y,z,0.0) - variance /= n-1 - variance =sqrt(variance) - for i in range(n): - z[i]=z[i]/variance - return z - -def inverseCumul(p): - #Coefficients in rational approximations. - a = [-3.969683028665376e+01,2.209460984245205e+02,-2.759285104469687e+02,1.383577518672690e+02,-3.066479806614716e+01,2.506628277459239e+00] - - b = [-5.447609879822406e+01,1.615858368580409e+02,-1.556989798598866e+02,6.680131188771972e+01,-1.328068155288572e+01] - - c = [-7.784894002430293e-03,-3.223964580411365e-01,-2.400758277161838e+00,-2.549732539343734e+00,4.374664141464968e+00,2.938163982698783e+00] - - d = [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00] - - #Define break-points. - - p_low = 0.02425 - p_high = 1 - p_low - - #Rational approximation for lower region. - - if p > 0 and p < p_low: - q = sqrt(-2*log(p)) - x = (((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) / ((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1) - - - #Rational approximation for central region. - - elif p>= p_low and p <= p_high: - q = p - 0.5 - r = q*q - x = (((((a[0]*r+a[1])*r+a[2])*r+a[3])*r+a[4])*r+a[5])*q /(((((b[0]*r+b[1])*r+b[2])*r+b[3])*r+b[4])*r+1) - - #Rational approximation for upper region. - - elif p>p_high and p < 1: - q = sqrt(-2*log(1-p)) - x = -(((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) /((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1) - - else: - return None - - if p>0 and p < 1: - e = 0.5 * erfcc(-x/sqrt(2)) - p - u = e * sqrt(2*pi) * exp(x*x/2) - x = x - u/(1 + x*u/2) - return x - else: - return None - -def gmean(lst): - N = len(lst) - if N == 0: - return 0 - else: - return (reduce(lambda x,y: x+y, lst, 0.0))/N - -def gmedian(lst2): - lst = lst2[:] - N = len(lst) - if N == 0: - return 0 - else: - lst.sort() - if N % 2 == 0: - return (lst[N/2]+lst[(N-2)/2])/2.0 - else: - return lst[(N-1)/2] - -def gpercentile(lst2, np): - 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 findOutliers(vals): - - valsOnly = [] - dataXZ = vals[:] - for i in range(len(dataXZ)): - valsOnly.append(dataXZ[i][1]) - - data = [('', valsOnly[:])] - - for item in data: - itemvalue = item[1] - nValue = len(itemvalue) - catValue = [] - - for item2 in itemvalue: - try: - tstrain, tvalue = item2 - except: - tvalue = item2 - if nValue <= 4: - 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) - elif item >= upHinge + Hstep: - outlier.append(item) - else: - pass - - for item in catValue: - if item <= lowHinge - 2*Hstep: - extreme.append(item) - elif item <= lowHinge - Hstep: - outlier.append(item) - else: - pass - 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 - plotHeight = canvas.size[1] - yTopOffset - yBottomOffset - iValues = [] - for item in data: - for item2 in item[1]: - try: - iValues.append(item2[1]) - except: - iValues.append(item2) - - #draw frame - max_Y = max(iValues) - min_Y = min(iValues) - scaleY = detScale(min_Y, max_Y) - Yll = scaleY[0] - Yur = scaleY[1] - nStep = scaleY[2] - stepY = (Yur - Yll)/nStep - stepYPixel = plotHeight/(nStep) - canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset) - - ##draw Y Scale - YYY = Yll - YCoord = plotHeight + yTopOffset - scaleFont=pid.Font(ttf="cour",size=11,bold=1) - for i in range(nStep+1): - strY = cformat(d=YYY, rank=0) - YCoord = max(YCoord, yTopOffset) - canvas.drawLine(xLeftOffset,YCoord,xLeftOffset-5,YCoord) - canvas.drawString(strY, xLeftOffset -30,YCoord +5,font=scaleFont) - YYY += stepY - YCoord -= stepYPixel - - ##draw X Scale - stepX = plotWidth/len(data) - XCoord = xLeftOffset + 0.5*stepX - YCoord = plotHeight + yTopOffset - scaleFont = pid.Font(ttf="tahoma",size=12,bold=0) - labelFont = pid.Font(ttf="tahoma",size=13,bold=0) - for item in data: - itemname, itemvalue = item - canvas.drawLine(XCoord, YCoord,XCoord, YCoord+5, color=pid.black) - canvas.drawString(itemname, XCoord - canvas.stringWidth(itemname,font=labelFont)/2.0,\ - YCoord +20,font=labelFont) - - nValue = len(itemvalue) - catValue = [] - for item2 in itemvalue: - try: - tstrain, tvalue = item2 - except: - tvalue = item2 - if nValue <= 4: - canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5) - else: - catValue.append(tvalue) - if catValue != []: - catMean = gmean(catValue) - catMedian = gmedian(catValue) - lowHinge = gpercentile(catValue, 25) - upHinge = gpercentile(catValue, 75) - Hstep = 1.5*(upHinge - lowHinge) - - outlier = [] - extrem = [] - - upperAdj = None - for item in catValue: - if item >= upHinge + 2*Hstep: - extrem.append(item) - elif item >= upHinge + Hstep: - outlier.append(item) - elif item > upHinge and item < upHinge + Hstep: - if upperAdj == None or item > upperAdj: - upperAdj = item - else: - pass - lowerAdj = None - for item in catValue: - if item <= lowHinge - 2*Hstep: - extrem.append(item) - elif item <= lowHinge - Hstep: - outlier.append(item) - if item < lowHinge and item > lowHinge - Hstep: - if lowerAdj == None or item < lowerAdj: - lowerAdj = item - else: - pass - canvas.drawRect(XCoord-20, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \ - XCoord+20, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll)) - canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll), \ - XCoord+20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll)) - if upperAdj != None: - canvas.drawLine(XCoord, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll), \ - XCoord, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll)) - canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll), \ - XCoord+20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll)) - if lowerAdj != None: - canvas.drawLine(XCoord, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \ - XCoord, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll)) - canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll), \ - XCoord+20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll)) - - outlierFont = pid.Font(ttf="cour",size=12,bold=0) - if outlier != []: - for item in outlier: - yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll) - #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3) - canvas.drawString('o', XCoord-3, yc+5, font=outlierFont, color=pid.orange) - if extrem != []: - for item in extrem: - yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll) - #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3) - canvas.drawString('*', XCoord-3, yc+6, font=outlierFont, color=pid.red) - - canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \ - color=pid.blue,size=3) - #print (catMean, catMedian, cat25per, cat75per) - pass - - XCoord += stepX - - labelFont=pid.Font(ttf="verdana",size=18,bold=0) - canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, \ - YCoord +40, font=labelFont) - canvas.drawString(YLabel,xLeftOffset-40, YCoord-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0,\ - font=labelFont, angle =90) - -def plotSecurity(canvas, text="12345"): - if not text: - return - - plotWidth = canvas.size[0] - plotHeight = canvas.size[1] - if plotHeight<=0 or plotWidth<=0: - return - - bgColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random()) - canvas.drawRect(0,0,plotWidth,plotHeight, edgeColor=bgColor, fillColor=bgColor) - - for i in range(30): - randomColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random()) - scaleFont=pid.Font(ttf="cour",size=random.choice(range(20, 50))) - canvas.drawString(random.choice('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'), - int(random.random()*plotWidth), int(random.random()*plotHeight), font=scaleFont, - color=randomColor, angle=random.choice(range(-45, 50))) - - step = (plotWidth-20)/len(text) - startX = 20 - for item in text: - randomColor = pid.Color(0.6*random.random(),0.6*random.random(), 0.6*random.random()) - scaleFont=pid.Font(ttf="verdana",size=random.choice(range(50, 60)),bold=1) - canvas.drawString(item, startX, plotHeight/2-10, font=scaleFont, - color=randomColor, angle=random.choice(range(-45, 50))) - startX += step - -# parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py) -# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py) -def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1): - - xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset - - plotWidth = canvas.size[0] - xLeftOffset - xRightOffset - plotHeight = canvas.size[1] - yTopOffset - yBottomOffset - if plotHeight<=0 or plotWidth<=0: - return - - if len(data) < 2: - return - - max_D = max(data) - min_D = min(data) - #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong - if max_D == float('inf') or max_D>webqtlConfig.MAXLRS: - max_D=webqtlConfig.MAXLRS #maximum LRS value - - xLow, xTop, stepX = detScale(min_D, max_D) - - #reduce data - step = ceil((xTop-xLow)/50.0) - j = xLow - dataXY = [] - Count = [] - while j <= xTop: - dataXY.append(j) - Count.append(0) - j += step - - for i, item in enumerate(data): - if item == float('inf') or item>webqtlConfig.MAXLRS: - item = webqtlConfig.MAXLRS #maximum LRS value - j = int((item-xLow)/step) - Count[j] += 1 - - yLow, yTop, stepY=detScale(0,max(Count)) - - #draw data - xScale = plotWidth/(xTop-xLow) - yScale = plotHeight/(yTop-yLow) - barWidth = xScale*step - - for i, count in enumerate(Count): - if count: - xc = (dataXY[i]-xLow)*xScale+xLeftOffset - yc =-(count-yLow)*yScale+yTopOffset+plotHeight - canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor) - - #draw drawing region - canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight) - - #draw scale - scaleFont=pid.Font(ttf="cour",size=11,bold=1) - x=xLow - for i in range(stepX+1): - xc=xLeftOffset+(x-xLow)*xScale - canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor) - strX = cformat(d=x, rank=0) - canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont) - x+= (xTop - xLow)/stepX - - y=yLow - for i in range(stepY+1): - yc=yTopOffset+plotHeight-(y-yLow)*yScale - canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor) - strY = "%d" %y - canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont) - y+= (yTop - yLow)/stepY - - #draw label - labelFont=pid.Font(ttf="tahoma",size=17,bold=0) - if XLabel: - canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0, - yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor) - - if YLabel: - canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0, - font=labelFont,color=labelColor,angle=90) - - labelFont=pid.Font(ttf="verdana",size=16,bold=0) - if title: - canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0, - 20,font=labelFont,color=labelColor) - -def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, sLabel = None, offset= (80, 20, 40, 100), barSpace = 2, zoom = 1): - xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset - plotWidth = canvas.size[0] - xLeftOffset - xRightOffset - plotHeight = canvas.size[1] - yTopOffset - yBottomOffset - if plotHeight<=0 or plotWidth<=0: - return - - NNN = len(data) - if NNN < 2 or NNN != len(label): - return - if variance and len(variance)!=NNN: - variance = [] - - Y2 = data[:] - if variance: - for i in range(NNN): - if variance[i]: - Y2 += [data[i]-variance[i]] - - #Y axis - YLow, YTop, stepY = detScale(min(Y2), max(Y2)) - YScale = plotHeight/(YTop - YLow) - - if YLow < 0 and YTop > 0: - drawZero = 1 - else: - drawZero = 0 - - #X axis - X = range(NNN) - Xll= 0 - Xur= NNN-1 - - - if drawZero: - YZero = yTopOffset+plotHeight-YScale*(0-YLow) - canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero) - else: - YZero = yTopOffset+plotHeight - #draw data - spaceWidth = barSpace - if spaceWidth < 1: - spaceWidth = 1 - barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN) - - xc= xLeftOffset - scaleFont=pid.Font(ttf="verdana",size=11,bold=0) - for i in range(NNN): - yc = yTopOffset+plotHeight-(data[i]-YLow)*YScale - canvas.drawRect(xc,YZero,xc+barWidth-1, yc, edgeColor=barColor,fillColor=barColor) - if variance and variance[i]: - varlen = variance[i]*YScale - if yc-varlen < yTopOffset: - topYd = yTopOffset - else: - topYd = yc-varlen - canvas.drawLine(xc+barWidth/2-2,yc-varlen,xc+barWidth/2+2,yc-varlen,color=pid.red) - canvas.drawLine(xc+barWidth/2,yc+varlen,xc+barWidth/2,topYd,color=pid.red) - canvas.drawLine(xc+barWidth/2-2,yc+varlen,xc+barWidth/2+2,yc+varlen,color=pid.red) - strX = label[i] - canvas.drawString(strX,xc+barWidth/2.0+2,yTopOffset+plotHeight+2+canvas.stringWidth(strX,font=scaleFont),font=scaleFont,angle=90) - xc += barWidth + spaceWidth - - #draw drawing region - canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight) - - #draw Y scale - scaleFont=pid.Font(ttf="cour",size=16,bold=1) - y=YLow - for i in range(stepY+1): - yc=yTopOffset+plotHeight-(y-YLow)*YScale - canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor) - strY = cformat(d=y, rank=0) - canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont) - y+= (YTop - YLow)/stepY - - #draw label - labelFont=pid.Font(ttf="verdana",size=17,bold=0) - if XLabel: - canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,yTopOffset+plotHeight+65,font=labelFont,color=labelColor) - - if YLabel: - canvas.drawString(YLabel,xLeftOffset-50, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,font=labelFont,color=labelColor,angle=90) - - labelFont=pid.Font(ttf="verdana",size=18,bold=0) - if title: - canvas.drawString(title,xLeftOffset,yTopOffset-15,font=labelFont,color=labelColor) - - return - -def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, axesColor=pid.black, labelColor=pid.black, lineSize="thin", lineColor=pid.grey, idFont="arial", idColor=pid.blue, idSize="14", symbolColor=pid.black, symbolType="circle", filled="yes", symbolSize="tiny", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1, bufferSpace = 15): - 'displayR : correlation scatter plot, loadings : loading plot' - - dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX)) - - #get ID font size - idFontSize = int(idSize) - - #If filled is yes, set fill color - if filled == "yes": - fillColor = symbolColor - else: - fillColor = None - - if symbolSize == "large": - sizeModifier = 7 - fontModifier = 12 - elif symbolSize == "medium": - sizeModifier = 5 - fontModifier = 8 - elif symbolSize == "small": - sizeModifier = 3 - fontModifier = 3 - else: - sizeModifier = 1 - fontModifier = -1 - - if rank == 0: # Pearson correlation - bufferSpace = 0 - dataXPrimary = dataX - dataYPrimary = dataY - dataXAlt = dataXRanked #Values used just for printing the other corr type to the graph image - dataYAlt = dataYRanked #Values used just for printing the other corr type to the graph image - else: # Spearman correlation: Switching Ranked and Unranked X and Y values - dataXPrimary = dataXRanked - dataYPrimary = dataYRanked - dataXAlt = dataX #Values used just for printing the other corr type to the graph image - dataYAlt = dataY #Values used just for printing the other corr type to the graph image - - xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset - plotWidth = canvas.size[0] - xLeftOffset - xRightOffset - plotHeight = canvas.size[1] - yTopOffset - yBottomOffset - if plotHeight<=0 or plotWidth<=0: - return - if len(dataXPrimary) < 1 or len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)): - return - - max_X=max(dataXPrimary) - min_X=min(dataXPrimary) - max_Y=max(dataYPrimary) - min_Y=min(dataYPrimary) - - #for some reason I forgot why I need to do this - if loadingPlot: - min_X = min(-0.1,min_X) - max_X = max(0.1,max_X) - min_Y = min(-0.1,min_Y) - max_Y = max(0.1,max_Y) - - xLow, xTop, stepX=detScale(min_X,max_X) - yLow, yTop, stepY=detScale(min_Y,max_Y) - xScale = plotWidth/(xTop-xLow) - yScale = plotHeight/(yTop-yLow) - - #draw drawing region - canvas.drawRect(xLeftOffset-bufferSpace, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace) - canvas.drawRect(xLeftOffset-bufferSpace+1, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace-1) - - #calculate data points - data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary) - xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary) - - labelFont=pid.Font(ttf=idFont,size=idFontSize,bold=0) - - if loadingPlot: - xZero = -xLow*xScale+xLeftOffset - yZero = yTopOffset+plotHeight+yLow*yScale - for point in xCoord: - canvas.drawLine(xZero,yZero,point[0],point[1],color=pid.red) - else: - if connectdot: - canvas.drawPolygon(xCoord,edgeColor=plotColor,closed=0) - else: - pass - - symbolFont = pid.Font(ttf="fnt_bs", size=12+fontModifier,bold=0) - - for i, item in enumerate(xCoord): - if dataLabel and dataLabel[i] in specialCases: - canvas.drawRect(item[0]-3, item[1]-3, item[0]+3, item[1]+3, edgeColor=pid.green) - #canvas.drawCross(item[0],item[1],color=pid.blue,size=5) - else: - if symbolType == "vertRect": - canvas.drawRect(x1=item[0]-sizeModifier+2,y1=item[1]-sizeModifier-2, x2=item[0]+sizeModifier-1,y2=item[1]+sizeModifier+2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor) - elif (symbolType == "circle" and filled != "yes"): - canvas.drawString(":", item[0]-canvas.stringWidth(":",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont) - elif (symbolType == "circle" and filled == "yes"): - canvas.drawString("5", item[0]-canvas.stringWidth("5",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont) - elif symbolType == "horiRect": - canvas.drawRect(x1=item[0]-sizeModifier-1,y1=item[1]-sizeModifier+3, x2=item[0]+sizeModifier+3,y2=item[1]+sizeModifier-2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor) - elif (symbolType == "square"): - canvas.drawRect(x1=item[0]-sizeModifier+1,y1=item[1]-sizeModifier-4, x2=item[0]+sizeModifier+2,y2=item[1]+sizeModifier-3, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor) - elif (symbolType == "diamond" and filled != "yes"): - canvas.drawString(",", item[0]-canvas.stringWidth(",",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor) - elif (symbolType == "diamond" and filled == "yes"): - canvas.drawString("D", item[0]-canvas.stringWidth("D",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor) - elif symbolType == "4-star": - canvas.drawString("l", item[0]-canvas.stringWidth("l",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor) - elif symbolType == "3-star": - canvas.drawString("k", item[0]-canvas.stringWidth("k",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor) - else: - canvas.drawCross(item[0],item[1]-2,color=symbolColor, size=sizeModifier+2) - - if showLabel and dataLabel: - if (symbolType == "vertRect" or symbolType == "diamond"): - labelGap = 15 - elif (symbolType == "4-star" or symbolType == "3-star"): - labelGap = 12 - else: - labelGap = 11 - canvas.drawString(dataLabel[i], item[0]- canvas.stringWidth(dataLabel[i], - font=labelFont)/2 + 1, item[1]+(labelGap+sizeModifier+(idFontSize-12)), font=labelFont, color=idColor) - - #draw scale - scaleFont=pid.Font(ttf="cour",size=16,bold=1) - - - x=xLow - for i in range(stepX+1): - xc=xLeftOffset+(x-xLow)*xScale - if ((x == 0) & (rank == 1)): - pass - else: - canvas.drawLine(xc,yTopOffset+plotHeight + bufferSpace,xc,yTopOffset+plotHeight+5 + bufferSpace, color=axesColor) - strX = cformat(d=x, rank=rank) - if ((strX == "0") & (rank == 1)): - pass - else: - canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+20 + bufferSpace,font=scaleFont) - x+= (xTop - xLow)/stepX - - y=yLow - for i in range(stepY+1): - yc=yTopOffset+plotHeight-(y-yLow)*yScale - if ((y == 0) & (rank == 1)): - pass - else: - canvas.drawLine(xLeftOffset - bufferSpace,yc,xLeftOffset-5 - bufferSpace,yc, color=axesColor) - strY = cformat(d=y, rank=rank) - if ((strY == "0") & (rank == 1)): - pass - else: - canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)- 10 - bufferSpace,yc+4,font=scaleFont) - y+= (yTop - yLow)/stepY - - #draw label - - labelFont=pid.Font(ttf="verdana",size=canvas.size[0]/45,bold=0) - titleFont=pid.Font(ttf="verdana",size=canvas.size[0]/40,bold=0) - - if (rank == 1 and not title): - canvas.drawString("Spearman Rank Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Spearman Rank Correlation",font=titleFont))/2.0, - 25,font=titleFont,color=labelColor) - elif (rank == 0 and not title): - canvas.drawString("Pearson Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Pearson Correlation",font=titleFont))/2.0, - 25,font=titleFont,color=labelColor) - - if XLabel: - canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0, - yTopOffset+plotHeight+yBottomOffset-25,font=labelFont,color=labelColor) - - if YLabel: - canvas.drawString(YLabel, xLeftOffset-65, yTopOffset+plotHeight- (plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0, - font=labelFont,color=labelColor,angle=90) - - labelFont=pid.Font(ttf="verdana",size=20,bold=0) - if title: - canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0, - 20,font=labelFont,color=labelColor) - - if fitcurve: - import sys - sys.argv = [ "mod_python" ] - #from numarray import linear_algebra as la - #from numarray import ones, array, dot, swapaxes - fitYY = array(dataYPrimary) - fitXX = array([ones(len(dataXPrimary)),dataXPrimary]) - AA = dot(fitXX,swapaxes(fitXX,0,1)) - BB = dot(fitXX,fitYY) - bb = la.linear_least_squares(AA,BB)[0] - - xc1 = xLeftOffset - yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale - if yc1 > yTopOffset+plotHeight: - yc1 = yTopOffset+plotHeight - xc1 = (yLow-bb[0])/bb[1] - xc1=(xc1-xLow)*xScale+xLeftOffset - elif yc1 < yTopOffset: - yc1 = yTopOffset - xc1 = (yTop-bb[0])/bb[1] - xc1=(xc1-xLow)*xScale+xLeftOffset - else: - pass - - xc2 = xLeftOffset + plotWidth - yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale - if yc2 > yTopOffset+plotHeight: - yc2 = yTopOffset+plotHeight - xc2 = (yLow-bb[0])/bb[1] - xc2=(xc2-xLow)*xScale+xLeftOffset - elif yc2 < yTopOffset: - yc2 = yTopOffset - xc2 = (yTop-bb[0])/bb[1] - xc2=(xc2-xLow)*xScale+xLeftOffset - else: - pass - - canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace,xc2,yc2,color=lineColor) - if lineSize == "medium": - canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor) - if lineSize == "thick": - canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor) - canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace-1,xc2,yc2-1,color=lineColor) - - - if displayR: - labelFont=pid.Font(ttf="trebuc",size=canvas.size[0]/60,bold=0) - NNN = len(dataX) - corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0] - - if NNN < 3: - corrPValue = 1.0 - else: - if abs(corr) >= 1.0: - corrPValue = 0.0 - else: - ZValue = 0.5*log((1.0+corr)/(1.0-corr)) - ZValue = ZValue*sqrt(NNN-3) - corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue))) - - NStr = "N = %d" % NNN - strLenN = canvas.stringWidth(NStr,font=labelFont) - - if rank == 1: - if corrPValue < 0.0000000000000001: - corrStr = "Rho = %1.3f P < 1.00 E-16" % (corr) - else: - corrStr = "Rho = %1.3f P = %3.2E" % (corr, corrPValue) - else: - if corrPValue < 0.0000000000000001: - corrStr = "r = %1.3f P < 1.00 E-16" % (corr) - else: - corrStr = "r = %1.3f P = %3.2E" % (corr, corrPValue) - strLen = canvas.stringWidth(corrStr,font=labelFont) - - canvas.drawString(NStr,xLeftOffset,yTopOffset-10,font=labelFont,color=labelColor) - canvas.drawString(corrStr,xLeftOffset+plotWidth-strLen,yTopOffset-10,font=labelFont,color=labelColor) - - return xCoord - -def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black", axesColor="black", labelColor="black", symbolColor="red", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1): - 'displayR : correlation scatter plot, loadings : loading plot' - - dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX)) - - # Switching Ranked and Unranked X and Y values if a Spearman Rank Correlation - if rank == 0: - dataXPrimary = dataX - dataYPrimary = dataY - dataXAlt = dataXRanked - dataYAlt = dataYRanked - - else: - dataXPrimary = dataXRanked - dataYPrimary = dataYRanked - dataXAlt = dataX - dataYAlt = dataY - - - - xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset - plotWidth = drawSpace.attributes['width'] - xLeftOffset - xRightOffset - plotHeight = drawSpace.attributes['height'] - yTopOffset - yBottomOffset - if plotHeight<=0 or plotWidth<=0: - return - if len(dataXPrimary) < 1 or len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)): - return - - max_X=max(dataXPrimary) - min_X=min(dataXPrimary) - max_Y=max(dataYPrimary) - min_Y=min(dataYPrimary) - - #for some reason I forgot why I need to do this - if loadingPlot: - min_X = min(-0.1,min_X) - max_X = max(0.1,max_X) - min_Y = min(-0.1,min_Y) - max_Y = max(0.1,max_Y) - - xLow, xTop, stepX=detScale(min_X,max_X) - yLow, yTop, stepY=detScale(min_Y,max_Y) - xScale = plotWidth/(xTop-xLow) - yScale = plotHeight/(yTop-yLow) - - #draw drawing region - r = svg.rect(xLeftOffset, yTopOffset, plotWidth, plotHeight, 'none', axesColor, 1) - drawSpace.addElement(r) - - #calculate data points - data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary) - xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary) - labelFontF = "verdana" - labelFontS = 11 - - if loadingPlot: - xZero = -xLow*xScale+xLeftOffset - yZero = yTopOffset+plotHeight+yLow*yScale - for point in xCoord: - drawSpace.addElement(svg.line(xZero,yZero,point[0],point[1], "red", 1)) - else: - if connectdot: - pass - #drawSpace.drawPolygon(xCoord,edgeColor=plotColor,closed=0) - else: - pass - - for i, item in enumerate(xCoord): - if dataLabel and dataLabel[i] in specialCases: - drawSpace.addElement(svg.rect(item[0]-3, item[1]-3, 6, 6, "none", "green", 0.5)) - #drawSpace.drawCross(item[0],item[1],color=pid.blue,size=5) - else: - drawSpace.addElement(svg.line(item[0],item[1]+5,item[0],item[1]-5,symbolColor,1)) - drawSpace.addElement(svg.line(item[0]+5,item[1],item[0]-5,item[1],symbolColor,1)) - if showLabel and dataLabel: - pass - drawSpace.addElement(svg.text(item[0], item[1]+14, dataLabel[i], labelFontS, - labelFontF, text_anchor="middle", style="stroke:blue;stroke-width:0.5;")) - #canvas.drawString(, item[0]- canvas.stringWidth(dataLabel[i], - # font=labelFont)/2, item[1]+14, font=labelFont, color=pid.blue) - - #draw scale - #scaleFont=pid.Font(ttf="cour",size=14,bold=1) - x=xLow - for i in range(stepX+1): - xc=xLeftOffset+(x-xLow)*xScale - drawSpace.addElement(svg.line(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, axesColor, 1)) - strX = cformat(d=x, rank=rank) - drawSpace.addElement(svg.text(xc,yTopOffset+plotHeight+20,strX,13, "courier", text_anchor="middle")) - x+= (xTop - xLow)/stepX - - y=yLow - for i in range(stepY+1): - yc=yTopOffset+plotHeight-(y-yLow)*yScale - drawSpace.addElement(svg.line(xLeftOffset,yc,xLeftOffset-5,yc, axesColor, 1)) - strY = cformat(d=y, rank=rank) - drawSpace.addElement(svg.text(xLeftOffset-10,yc+5,strY,13, "courier", text_anchor="end")) - y+= (yTop - yLow)/stepY - - #draw label - labelFontF = "verdana" - labelFontS = 17 - if XLabel: - drawSpace.addElement(svg.text(xLeftOffset+plotWidth/2.0, - yTopOffset+plotHeight+yBottomOffset-10,XLabel, - labelFontS, labelFontF, text_anchor="middle")) - - if YLabel: - drawSpace.addElement(svg.text(xLeftOffset-50, - yTopOffset+plotHeight/2,YLabel, - labelFontS, labelFontF, text_anchor="middle", style="writing-mode:tb-rl", transform="rotate(270 %d %d)" % (xLeftOffset-50, yTopOffset+plotHeight/2))) - #drawSpace.drawString(YLabel, xLeftOffset-50, yTopOffset+plotHeight- (plotHeight-drawSpace.stringWidth(YLabel,font=labelFont))/2.0, - # font=labelFont,color=labelColor,angle=90) - - - if fitcurve: - sys.argv = [ "mod_python" ] - #from numarray import linear_algebra as la - #from numarray import ones, array, dot, swapaxes - fitYY = array(dataYPrimary) - fitXX = array([ones(len(dataXPrimary)),dataXPrimary]) - AA = dot(fitXX,swapaxes(fitXX,0,1)) - BB = dot(fitXX,fitYY) - bb = la.linear_least_squares(AA,BB)[0] - - xc1 = xLeftOffset - yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale - if yc1 > yTopOffset+plotHeight: - yc1 = yTopOffset+plotHeight - xc1 = (yLow-bb[0])/bb[1] - xc1=(xc1-xLow)*xScale+xLeftOffset - elif yc1 < yTopOffset: - yc1 = yTopOffset - xc1 = (yTop-bb[0])/bb[1] - xc1=(xc1-xLow)*xScale+xLeftOffset - else: - pass - - xc2 = xLeftOffset + plotWidth - yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale - if yc2 > yTopOffset+plotHeight: - yc2 = yTopOffset+plotHeight - xc2 = (yLow-bb[0])/bb[1] - xc2=(xc2-xLow)*xScale+xLeftOffset - elif yc2 < yTopOffset: - yc2 = yTopOffset - xc2 = (yTop-bb[0])/bb[1] - xc2=(xc2-xLow)*xScale+xLeftOffset - else: - pass - - drawSpace.addElement(svg.line(xc1,yc1,xc2,yc2,"green", 1)) - - if displayR: - labelFontF = "trebuc" - labelFontS = 14 - NNN = len(dataX) - - corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0] - - if NNN < 3: - corrPValue = 1.0 - else: - if abs(corr) >= 1.0: - corrPValue = 0.0 - else: - ZValue = 0.5*log((1.0+corr)/(1.0-corr)) - ZValue = ZValue*sqrt(NNN-3) - corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue))) - - NStr = "N of Cases=%d" % NNN - - if rank == 1: - corrStr = "Spearman's r=%1.3f P=%3.2E" % (corr, corrPValue) - else: - corrStr = "Pearson's r=%1.3f P=%3.2E" % (corr, corrPValue) - - drawSpace.addElement(svg.text(xLeftOffset,yTopOffset-10,NStr, - labelFontS, labelFontF, text_anchor="start")) - drawSpace.addElement(svg.text(xLeftOffset+plotWidth,yTopOffset-25,corrStr, - labelFontS, labelFontF, text_anchor="end")) - """ - """ - return - - -# This function determines the scale of the plot -def detScaleOld(min,max): - if min>=max: - return None - elif min == -1.0 and max == 1.0: - return [-1.2,1.2,12] - else: - a=max-min - b=floor(log10(a)) - c=pow(10.0,b) - if a < c*5.0: - c/=2.0 - #print a,b,c - low=c*floor(min/c) - high=c*ceil(max/c) - return [low,high,round((high-low)/c)] - -def detScale(min=0,max=0,bufferSpace=3): - - if min>=max: - return None - elif min == -1.0 and max == 1.0: - return [-1.2,1.2,12] - else: - a=max-min - if max != 0: - max += 0.1*a - if min != 0: - if min > 0 and min < 0.1*a: - min = 0.0 - else: - min -= 0.1*a - a=max-min - b=floor(log10(a)) - c=pow(10.0,b) - low=c*floor(min/c) - high=c*ceil(max/c) - n = round((high-low)/c) - div = 2.0 - while n < 5 or n > 15: - if n < 5: - c /= div - else: - c *= div - if div == 2.0: - div =5.0 - else: - div =2.0 - low=c*floor(min/c) - high=c*ceil(max/c) - n = round((high-low)/c) - - return [low,high,n] - - - -def colorSpectrumOld(n): - if n == 1: - return [pid.Color(1,0,0)] - elif n == 2: - return [pid.Color(1,0,0),pid.Color(0,0,1)] - elif n == 3: - return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)] - else: - step = 2.0/(n-1) - red = 1.0 - green = 0.0 - blue = 0.0 - colors = [pid.Color(red,green,blue)] - i = 1 - greenpeak = 0 - while i < n: - if red >= step: - red -= step - green += step - if green >= 1.0: - greenpeak = 1 - blue += green -1.0 - green = 1.0 - else: - red = 0.0 - if greenpeak: - green -= step - blue += step - else: - green += step - if green >= 1.0: - greenpeak = 1 - blue += green -1.0 - green = 2.0 -green - elif green < 0.0: - green = 0.0 - else: - pass - colors.append(pid.Color(red,green,blue)) - i += 1 - return colors - - - - -def bluefunc(x): - return 1.0 / (1.0 + exp(-10*(x-0.6))) - - -def redfunc(x): - return 1.0 / (1.0 + exp(10*(x-0.5))) - -def greenfunc(x): - return 1 - pow(redfunc(x+0.2),2) - bluefunc(x-0.3) - -def colorSpectrum(n=100): - multiple = 10 - if n == 1: - return [pid.Color(1,0,0)] - elif n == 2: - return [pid.Color(1,0,0),pid.Color(0,0,1)] - elif n == 3: - return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)] - N = n*multiple - out = [None]*N; - for i in range(N): - x = float(i)/N - out[i] = pid.Color(redfunc(x), greenfunc(x), bluefunc(x)); - out2 = [out[0]] - step = N/float(n-1) - j = 0 - for i in range(n-2): - j += step - out2.append(out[int(j)]) - out2.append(out[-1]) - return out2 - - -def colorSpectrumSVG(n=100): - multiple = 10 - if n == 1: - return ["rgb(255,0,0)"] - elif n == 2: - return ["rgb(255,0,0)","rgb(0,0,255)"] - elif n == 3: - return ["rgb(255,0,0)","rgb(0,255,0)","rgb(0,0,255)"] - N = n*multiple - out = [None]*N; - for i in range(N): - x = float(i)/N - out[i] = "rgb(%d, %d, %d)" % (redfunc(x)*255, greenfunc(x)*255, bluefunc(x)*255); - out2 = [out[0]] - step = N/float(n-1) - j = 0 - for i in range(n-2): - j += step - out2.append(out[int(j)]) - out2.append(out[-1]) - return out2 - - -def BWSpectrum(n=100): - multiple = 10 - if n == 1: - return [pid.Color(0,0,0)] - elif n == 2: - return [pid.Color(0,0,0),pid.Color(1,1,1)] - elif n == 3: - return [pid.Color(0,0,0),pid.Color(0.5,0.5,0.5),pid.Color(1,1,1)] - - step = 1.0/n - x = 0.0 - out = [] - for i in range(n): - out.append(pid.Color(x,x,x)); - x += step - return out diff --git a/web/webqtl/utility/TDCell.py b/web/webqtl/utility/TDCell.py deleted file mode 100755 index 76b9c5db..00000000 --- a/web/webqtl/utility/TDCell.py +++ /dev/null @@ -1,42 +0,0 @@ -# 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 - -########################################################## -# -# Table Cell Class -# -########################################################## - - -class TDCell: - def __init__(self, html="", text="", val=0.0): - self.html = html #html, for web page - self.text = text #text value, for output to a text file - self.val = val #sort by value - - def __str__(self): - return self.text - diff --git a/web/webqtl/utility/THCell.py b/web/webqtl/utility/THCell.py deleted file mode 100755 index a96b9e49..00000000 --- a/web/webqtl/utility/THCell.py +++ /dev/null @@ -1,44 +0,0 @@ -# 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 - -########################################################## -# -# Table Header Class -# -########################################################## - - -class THCell: - def __init__(self, html="", text="", sort=1, idx=-1): - self.html = html #html, for web page - self.text = text #Column text value - self.sort = sort #0: not sortable, 1: yes - self.idx = idx #sort by value - - def __str__(self): - return self.text - - diff --git a/web/webqtl/utility/__init__.py b/web/webqtl/utility/__init__.py deleted file mode 100755 index e69de29b..00000000 --- a/web/webqtl/utility/__init__.py +++ /dev/null diff --git a/web/webqtl/utility/svg.py b/web/webqtl/utility/svg.py deleted file mode 100755 index e49a6c3c..00000000 --- a/web/webqtl/utility/svg.py +++ /dev/null @@ -1,1069 +0,0 @@ -# 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 - -#!/usr/bin/env python -##Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen) -##All rights reserved. -## -##Redistribution and use in source and binary forms, with or without modification, -##are permitted provided that the following conditions are met: -## -##Redistributions of source code must retain the above copyright notice, this -##list of conditions and the following disclaimer. -## -##Redistributions in binary form must reproduce the above copyright notice, -##this list of conditions and the following disclaimer in the documentation and/or -##other materials provided with the distribution. -## -##Neither the name of the Stichting Farmaceutische Kengetallen nor the names of -##its contributors may be used to endorse or promote products derived from this -##software without specific prior written permission. -## -##THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -##AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -##IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -##DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE -##FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -##DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -##SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -##CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -##OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -##OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -##Thanks to Gerald Rosennfellner for his help and useful comments. - -__doc__="""Use SVGdraw to generate your SVGdrawings. - -SVGdraw uses an object model drawing and a method toXML to create SVG graphics -by using easy to use classes and methods usualy you start by creating a drawing eg - - d=drawing() - #then you create a SVG root element - s=svg() - #then you add some elements eg a circle and add it to the svg root element - c=circle() - #you can supply attributes by using named arguments. - c=circle(fill='red',stroke='blue') - #or by updating the attributes attribute: - c.attributes['stroke-width']=1 - s.addElement(c) - #then you add the svg root element to the drawing - d.setSVG(s) - #and finaly you xmlify the drawing - d.toXml() - - -this results in the svg source of the drawing, which consists of a circle -on a white background. Its as easy as that;) -This module was created using the SVG specification of www.w3c.org and the -O'Reilly (www.oreilly.com) python books as information sources. A svg viewer -is available from www.adobe.com""" - -__version__="1.0" - -# there are two possibilities to generate svg: -# via a dom implementation and directly using <element>text</element> strings -# the latter is way faster (and shorter in coding) -# the former is only used in debugging svg programs -# maybe it will be removed alltogether after a while -# with the following variable you indicate whether to use the dom implementation -# Note that PyXML is required for using the dom implementation. -# It is also possible to use the standard minidom. But I didn't try that one. -# Anyway the text based approach is about 60 times faster than using the full dom implementation. -use_dom_implementation=0 - - -import exceptions -if use_dom_implementation<>0: - try: - from xml.dom import implementation - from xml.dom.ext import PrettyPrint - except: - raise exceptions.ImportError, "PyXML is required for using the dom implementation" -#The implementation is used for the creating the XML document. -#The prettyprint module is used for converting the xml document object to a xml file - -import sys -assert sys.version_info[0]>=2 -if sys.version_info[1]<2: - True=1 - False=0 - file=open - -sys.setrecursionlimit=50 -#The recursion limit is set conservative so mistakes like s=svg() s.addElement(s) -#won't eat up too much processor time. - -#the following code is pasted form xml.sax.saxutils -#it makes it possible to run the code without the xml sax package installed -#To make it possible to have <rubbish> in your text elements, it is necessary to escape the texts -def _escape(data, entities={}): - """Escape &, <, and > in a string of data. - - You can escape other strings of data by passing a dictionary as - the optional entities parameter. The keys and values must all be - strings; each key will be replaced with its corresponding value. - """ - #data = data.replace("&", "&") - data = data.replace("<", "<") - data = data.replace(">", ">") - for chars, entity in entities.items(): - data = data.replace(chars, entity) - return data - -def _quoteattr(data, entities={}): - """Escape and quote an attribute value. - - Escape &, <, and > in a string of data, then quote it for use as - an attribute value. The \" character will be escaped as well, if - necessary. - - You can escape other strings of data by passing a dictionary as - the optional entities parameter. The keys and values must all be - strings; each key will be replaced with its corresponding value. - """ - data = _escape(data, entities) - if '"' in data: - if "'" in data: - data = '"%s"' % data.replace('"', """) - else: - data = "'%s'" % data - else: - data = '"%s"' % data - return data - - - -def _xypointlist(a): - """formats a list of xy pairs""" - s='' - for e in a: #this could be done more elegant - s+=str(e)[1:-1] +' ' - return s - -def _viewboxlist(a): - """formats a tuple""" - s='' - for e in a: - s+=str(e)+' ' - return s - -def _pointlist(a): - """formats a list of numbers""" - return str(a)[1:-1] - -class pathdata: - """class used to create a pathdata object which can be used for a path. - although most methods are pretty straightforward it might be useful to look at the SVG specification.""" - #I didn't test the methods below. - def __init__(self,x=None,y=None): - self.path=[] - if x is not None and y is not None: - self.path.append('M '+str(x)+' '+str(y)) - def closepath(self): - """ends the path""" - self.path.append('z') - def move(self,x,y): - """move to absolute""" - self.path.append('M '+str(x)+' '+str(y)) - def relmove(self,x,y): - """move to relative""" - self.path.append('m '+str(x)+' '+str(y)) - def line(self,x,y): - """line to absolute""" - self.path.append('L '+str(x)+' '+str(y)) - def relline(self,x,y): - """line to relative""" - self.path.append('l '+str(x)+' '+str(y)) - def hline(self,x): - """horizontal line to absolute""" - self.path.append('H'+str(x)) - def relhline(self,x): - """horizontal line to relative""" - self.path.append('h'+str(x)) - def vline(self,y): - """verical line to absolute""" - self.path.append('V'+str(y)) - def relvline(self,y): - """vertical line to relative""" - self.path.append('v'+str(y)) - def bezier(self,x1,y1,x2,y2,x,y): - """bezier with xy1 and xy2 to xy absolut""" - self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def relbezier(self,x1,y1,x2,y2,x,y): - """bezier with xy1 and xy2 to xy relative""" - self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def smbezier(self,x2,y2,x,y): - """smooth bezier with xy2 to xy absolut""" - self.path.append('S'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def relsmbezier(self,x2,y2,x,y): - """smooth bezier with xy2 to xy relative""" - self.path.append('s'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def qbezier(self,x1,y1,x,y): - """quadratic bezier with xy1 to xy absolut""" - self.path.append('Q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) - def relqbezier(self,x1,y1,x,y): - """quadratic bezier with xy1 to xy relative""" - self.path.append('q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) - def smqbezier(self,x,y): - """smooth quadratic bezier to xy absolut""" - self.path.append('T'+str(x)+','+str(y)) - def relsmqbezier(self,x,y): - """smooth quadratic bezier to xy relative""" - self.path.append('t'+str(x)+','+str(y)) - def ellarc(self,rx,ry,xrot,laf,sf,x,y): - """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy absolut""" - self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) - def relellarc(self,rx,ry,xrot,laf,sf,x,y): - """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy relative""" - self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) - def __repr__(self): - return ' '.join(self.path) - - - - -class SVGelement: - """SVGelement(type,attributes,elements,text,namespace,**args) - Creates a arbitrary svg element and is intended to be subclassed not used on its own. - This element is the base of every svg element it defines a class which resembles - a xml-element. The main advantage of this kind of implementation is that you don't - have to create a toXML method for every different graph object. Every element - consists of a type, attribute, optional subelements, optional text and an optional - namespace. Note the elements==None, if elements = None:self.elements=[] construction. - This is done because if you default to elements=[] every object has a reference - to the same empty list.""" - def __init__(self,type='',attributes=None,elements=None,text='',namespace='',cdata=None, **args): - self.type=type - if attributes==None: - self.attributes={} - else: - self.attributes=attributes - if elements==None: - self.elements=[] - else: - self.elements=elements - self.text=text - self.namespace=namespace - self.cdata=cdata - for arg in args.keys(): - arg2 = arg.replace("__", ":") - arg2 = arg2.replace("_", "-") - self.attributes[arg2]=args[arg] - def addElement(self,SVGelement): - """adds an element to a SVGelement - - SVGelement.addElement(SVGelement) - """ - self.elements.append(SVGelement) - - def toXml(self,level,f): - f.write('\t'*level) - f.write('<'+self.type) - for attkey in self.attributes.keys(): - f.write(' '+_escape(str(attkey))+'='+_quoteattr(str(self.attributes[attkey]))) - if self.namespace: - f.write(' xmlns="'+ _escape(str(self.namespace))+'" xmlns:xlink="http://www.w3.org/1999/xlink"') - if self.elements or self.text or self.cdata: - f.write('>') - if self.elements: - f.write('\n') - for element in self.elements: - element.toXml(level+1,f) - if self.cdata: - f.write('\n'+'\t'*(level+1)+'<![CDATA[') - for line in self.cdata.splitlines(): - f.write('\n'+'\t'*(level+2)+line) - f.write('\n'+'\t'*(level+1)+']]>\n') - if self.text: - if type(self.text)==type(''): #If the text is only text - f.write(_escape(str(self.text))) - else: #If the text is a spannedtext class - f.write(str(self.text)) - if self.elements: - f.write('\t'*level+'</'+self.type+'>\n') - elif self.text: - f.write('</'+self.type+'>\n') - elif self.cdata: - f.write('\t'*level+'</'+self.type+'>\n') - else: - f.write('/>\n') - -class tspan(SVGelement): - """ts=tspan(text='',**args) - - a tspan element can be used for applying formatting to a textsection - usage: - ts=tspan('this text is bold') - ts.attributes['font-weight']='bold' - st=spannedtext() - st.addtspan(ts) - t=text(3,5,st) - """ - def __init__(self,text=None,**args): - SVGelement.__init__(self,'tspan',**args) - if self.text<>None: - self.text=text - def __repr__(self): - s="<tspan" - for key,value in self.attributes.items(): - s+= ' %s="%s"' % (key,value) - s+='>' - s+=self.text - s+='</tspan>' - return s - -class tref(SVGelement): - """tr=tref(link='',**args) - - a tref element can be used for referencing text by a link to its id. - usage: - tr=tref('#linktotext') - st=spannedtext() - st.addtref(tr) - t=text(3,5,st) - """ - def __init__(self,link,**args): - SVGelement.__init__(self,'tref',{'xlink:href':link},**args) - def __repr__(self): - s="<tref" - - for key,value in self.attributes.items(): - s+= ' %s="%s"' % (key,value) - s+='/>' - return s - -class spannedtext: - """st=spannedtext(textlist=[]) - - a spannedtext can be used for text which consists of text, tspan's and tref's - You can use it to add to a text element or path element. Don't add it directly - to a svg or a group element. - usage: - - ts=tspan('this text is bold') - ts.attributes['font-weight']='bold' - tr=tref('#linktotext') - tr.attributes['fill']='red' - st=spannedtext() - st.addtspan(ts) - st.addtref(tr) - st.addtext('This text is not bold') - t=text(3,5,st) - """ - def __init__(self,textlist=None): - if textlist==None: - self.textlist=[] - else: - self.textlist=textlist - def addtext(self,text=''): - self.textlist.append(text) - def addtspan(self,tspan): - self.textlist.append(tspan) - def addtref(self,tref): - self.textlist.append(tref) - def __repr__(self): - s="" - for element in self.textlist: - s+=str(element) - return s - -class rect(SVGelement): - """r=rect(width,height,x,y,fill,stroke,stroke_width,**args) - - a rectangle is defined by a width and height and a xy pair - """ - def __init__(self,x=None,y=None,width=None,height=None,fill=None,stroke=None,stroke_width=None,**args): - if width==None or height==None: - if width<>None: - raise ValueError, 'height is required' - if height<>None: - raise ValueError, 'width is required' - else: - raise ValueError, 'both height and width are required' - SVGelement.__init__(self,'rect',{'width':width,'height':height},**args) - if x<>None: - self.attributes['x']=x - if y<>None: - self.attributes['y']=y - if fill<>None: - self.attributes['fill']=fill - if stroke<>None: - self.attributes['stroke']=stroke - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - -class ellipse(SVGelement): - """e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args) - - an ellipse is defined as a center and a x and y radius. - """ - def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args): - if rx==None or ry== None: - if rx<>None: - raise ValueError, 'rx is required' - if ry<>None: - raise ValueError, 'ry is required' - else: - raise ValueError, 'both rx and ry are required' - SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args) - if cx<>None: - self.attributes['cx']=cx - if cy<>None: - self.attributes['cy']=cy - if fill<>None: - self.attributes['fill']=fill - if stroke<>None: - self.attributes['stroke']=stroke - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - - -class circle(SVGelement): - """c=circle(x,y,radius,fill,stroke,stroke_width,**args) - - The circle creates an element using a x, y and radius values eg - """ - def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args): - if r==None: - raise ValueError, 'r is required' - SVGelement.__init__(self,'circle',{'r':r},**args) - if cx<>None: - self.attributes['cx']=cx - if cy<>None: - self.attributes['cy']=cy - if fill<>None: - self.attributes['fill']=fill - if stroke<>None: - self.attributes['stroke']=stroke - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - -class point(circle): - """p=point(x,y,color) - - A point is defined as a circle with a size 1 radius. It may be more efficient to use a - very small rectangle if you use many points because a circle is difficult to render. - """ - def __init__(self,x,y,fill='black',**args): - circle.__init__(self,x,y,1,fill,**args) - -class line(SVGelement): - """l=line(x1,y1,x2,y2,stroke,stroke_width,**args) - - A line is defined by a begin x,y pair and an end x,y pair - """ - def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'line',**args) - if x1<>None: - self.attributes['x1']=x1 - if y1<>None: - self.attributes['y1']=y1 - if x2<>None: - self.attributes['x2']=x2 - if y2<>None: - self.attributes['y2']=y2 - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - if stroke<>None: - self.attributes['stroke']=stroke - -class polyline(SVGelement): - """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args) - - a polyline is defined by a list of xy pairs - """ - def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'polyline',{'points':_xypointlist(points)},**args) - if fill<>None: - self.attributes['fill']=fill - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - if stroke<>None: - self.attributes['stroke']=stroke - -class polygon(SVGelement): - """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args) - - a polygon is defined by a list of xy pairs - """ - def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'polygon',{'points':_xypointlist(points)},**args) - if fill<>None: - self.attributes['fill']=fill - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - if stroke<>None: - self.attributes['stroke']=stroke - -class path(SVGelement): - """p=path(path,fill,stroke,stroke_width,**args) - - a path is defined by a path object and optional width, stroke and fillcolor - """ - def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args): - SVGelement.__init__(self,'path',{'d':str(pathdata)},**args) - if stroke<>None: - self.attributes['stroke']=stroke - if fill<>None: - self.attributes['fill']=fill - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - if id<>None: - self.attributes['id']=id - - -class text(SVGelement): - """t=text(x,y,text,font_size,font_family,**args) - - a text element can bge used for displaying text on the screen - """ - def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args): - SVGelement.__init__(self,'text',**args) - if x<>None: - self.attributes['x']=x - if y<>None: - self.attributes['y']=y - if font_size<>None: - self.attributes['font-size']=font_size - if font_family<>None: - self.attributes['font-family']=font_family - if text<>None: - self.text=text - if text_anchor<>None: - self.attributes['text-anchor']=text_anchor - - -class textpath(SVGelement): - """tp=textpath(text,link,**args) - - a textpath places a text on a path which is referenced by a link. - """ - def __init__(self,link,text=None,**args): - SVGelement.__init__(self,'textPath',{'xlink:href':link},**args) - if text<>None: - self.text=text - -class pattern(SVGelement): - """p=pattern(x,y,width,height,patternUnits,**args) - - A pattern is used to fill or stroke an object using a pre-defined - graphic object which can be replicated ("tiled") at fixed intervals - in x and y to cover the areas to be painted. - """ - def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args): - SVGelement.__init__(self,'pattern',**args) - if x<>None: - self.attributes['x']=x - if y<>None: - self.attributes['y']=y - if width<>None: - self.attributes['width']=width - if height<>None: - self.attributes['height']=height - if patternUnits<>None: - self.attributes['patternUnits']=patternUnits - -class title(SVGelement): - """t=title(text,**args) - - a title is a text element. The text is displayed in the title bar - add at least one to the root svg element - """ - def __init__(self,text=None,**args): - SVGelement.__init__(self,'title',**args) - if text<>None: - self.text=text - -class description(SVGelement): - """d=description(text,**args) - - a description can be added to any element and is used for a tooltip - Add this element before adding other elements. - """ - def __init__(self,text=None,**args): - SVGelement.__init__(self,'desc',**args) - if text<>None: - self.text=text - -class lineargradient(SVGelement): - """lg=lineargradient(x1,y1,x2,y2,id,**args) - - defines a lineargradient using two xy pairs. - stop elements van be added to define the gradient colors. - """ - def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args): - SVGelement.__init__(self,'linearGradient',**args) - if x1<>None: - self.attributes['x1']=x1 - if y1<>None: - self.attributes['y1']=y1 - if x2<>None: - self.attributes['x2']=x2 - if y2<>None: - self.attributes['y2']=y2 - if id<>None: - self.attributes['id']=id - -class radialgradient(SVGelement): - """rg=radialgradient(cx,cy,r,fx,fy,id,**args) - - defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint. - stop elements van be added to define the gradient colors. - """ - def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args): - SVGelement.__init__(self,'radialGradient',**args) - if cx<>None: - self.attributes['cx']=cx - if cy<>None: - self.attributes['cy']=cy - if r<>None: - self.attributes['r']=r - if fx<>None: - self.attributes['fx']=fx - if fy<>None: - self.attributes['fy']=fy - if id<>None: - self.attributes['id']=id - -class stop(SVGelement): - """st=stop(offset,stop_color,**args) - - Puts a stop color at the specified radius - """ - def __init__(self,offset,stop_color=None,**args): - SVGelement.__init__(self,'stop',{'offset':offset},**args) - if stop_color<>None: - self.attributes['stop-color']=stop_color - -class style(SVGelement): - """st=style(type,cdata=None,**args) - - Add a CDATA element to this element for defing in line stylesheets etc.. - """ - def __init__(self,type,cdata=None,**args): - SVGelement.__init__(self,'style',{'type':type},cdata=cdata, **args) - - -class image(SVGelement): - """im=image(url,width,height,x,y,**args) - - adds an image to the drawing. Supported formats are .png, .jpg and .svg. - """ - def __init__(self,url,x=None,y=None,width=None,height=None,**args): - if width==None or height==None: - if width<>None: - raise ValueError, 'height is required' - if height<>None: - raise ValueError, 'width is required' - else: - raise ValueError, 'both height and width are required' - SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args) - if x<>None: - self.attributes['x']=x - if y<>None: - self.attributes['y']=y - -class cursor(SVGelement): - """c=cursor(url,**args) - - defines a custom cursor for a element or a drawing - """ - def __init__(self,url,**args): - SVGelement.__init__(self,'cursor',{'xlink:href':url},**args) - - -class marker(SVGelement): - """m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args) - - defines a marker which can be used as an endpoint for a line or other pathtypes - add an element to it which should be used as a marker. - """ - def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args): - SVGelement.__init__(self,'marker',**args) - if id<>None: - self.attributes['id']=id - if viewBox<>None: - self.attributes['viewBox']=_viewboxlist(viewBox) - if refx<>None: - self.attributes['refX']=refx - if refy<>None: - self.attributes['refY']=refy - if markerWidth<>None: - self.attributes['markerWidth']=markerWidth - if markerHeight<>None: - self.attributes['markerHeight']=markerHeight - -class group(SVGelement): - """g=group(id,**args) - - a group is defined by an id and is used to contain elements - g.addElement(SVGelement) - """ - def __init__(self,id=None,**args): - SVGelement.__init__(self,'g',**args) - if id<>None: - self.attributes['id']=id - -class symbol(SVGelement): - """sy=symbol(id,viewbox,**args) - - defines a symbol which can be used on different places in your graph using - the use element. A symbol is not rendered but you can use 'use' elements to - display it by referencing its id. - sy.addElement(SVGelement) - """ - - def __init__(self,id=None,viewBox=None,**args): - SVGelement.__init__(self,'symbol',**args) - if id<>None: - self.attributes['id']=id - if viewBox<>None: - self.attributes['viewBox']=_viewboxlist(viewBox) - -class defs(SVGelement): - """d=defs(**args) - - container for defining elements - """ - def __init__(self,**args): - SVGelement.__init__(self,'defs',**args) - -class switch(SVGelement): - """sw=switch(**args) - - Elements added to a switch element which are "switched" by the attributes - requiredFeatures, requiredExtensions and systemLanguage. - Refer to the SVG specification for details. - """ - def __init__(self,**args): - SVGelement.__init__(self,'switch',**args) - - -class use(SVGelement): - """u=use(link,x,y,width,height,**args) - - references a symbol by linking to its id and its position, height and width - """ - def __init__(self,link,x=None,y=None,width=None,height=None,**args): - SVGelement.__init__(self,'use',{'xlink:href':link},**args) - if x<>None: - self.attributes['x']=x - if y<>None: - self.attributes['y']=y - - if width<>None: - self.attributes['width']=width - if height<>None: - self.attributes['height']=height - - -class link(SVGelement): - """a=link(url,**args) - - a link is defined by a hyperlink. add elements which have to be linked - a.addElement(SVGelement) - """ - def __init__(self,link='',**args): - SVGelement.__init__(self,'a',{'xlink:href':link},**args) - -class view(SVGelement): - """v=view(id,**args) - - a view can be used to create a view with different attributes""" - def __init__(self,id=None,**args): - SVGelement.__init__(self,'view',**args) - if id<>None: - self.attributes['id']=id - -class script(SVGelement): - """sc=script(type,type,cdata,**args) - - adds a script element which contains CDATA to the SVG drawing - - """ - def __init__(self,type,cdata=None,**args): - SVGelement.__init__(self,'script',{'type':type},cdata=cdata,**args) - -class animate(SVGelement): - """an=animate(attribute,from,to,during,**args) - - animates an attribute. - """ - def __init__(self,attribute,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animate',{'attributeName':attribute},**args) - if fr<>None: - self.attributes['from']=fr - if to<>None: - self.attributes['to']=to - if dur<>None: - self.attributes['dur']=dur - -class animateMotion(SVGelement): - """an=animateMotion(pathdata,dur,**args) - - animates a SVGelement over the given path in dur seconds - """ - def __init__(self,pathdata,dur,**args): - SVGelement.__init__(self,'animateMotion',**args) - if pathdata<>None: - self.attributes['path']=str(pathdata) - if dur<>None: - self.attributes['dur']=dur - -class animateTransform(SVGelement): - """antr=animateTransform(type,from,to,dur,**args) - - transform an element from and to a value. - """ - def __init__(self,type=None,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args) - #As far as I know the attributeName is always transform - if type<>None: - self.attributes['type']=type - if fr<>None: - self.attributes['from']=fr - if to<>None: - self.attributes['to']=to - if dur<>None: - self.attributes['dur']=dur -class animateColor(SVGelement): - """ac=animateColor(attribute,type,from,to,dur,**args) - - Animates the color of a element - """ - def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animateColor',{'attributeName':attribute},**args) - if type<>None: - self.attributes['type']=type - if fr<>None: - self.attributes['from']=fr - if to<>None: - self.attributes['to']=to - if dur<>None: - self.attributes['dur']=dur -class set(SVGelement): - """st=set(attribute,to,during,**args) - - sets an attribute to a value for a - """ - def __init__(self,attribute,to=None,dur=None,**args): - SVGelement.__init__(self,'set',{'attributeName':attribute},**args) - if to<>None: - self.attributes['to']=to - if dur<>None: - self.attributes['dur']=dur - - - -class svg(SVGelement): - """s=svg(viewbox,width,height,**args) - - a svg or element is the root of a drawing add all elements to a svg element. - You can have different svg elements in one svg file - s.addElement(SVGelement) - - eg - d=drawing() - s=svg((0,0,100,100),'100%','100%') - c=circle(50,50,20) - s.addElement(c) - d.setSVG(s) - d.toXml() - """ - def __init__(self,viewBox=None, width=None, height=None,**args): - SVGelement.__init__(self,'svg',**args) - if viewBox<>None: - self.attributes['viewBox']=_viewboxlist(viewBox) - if width<>None: - self.attributes['width']=width - if height<>None: - self.attributes['height']=height - self.namespace="http://www.w3.org/2000/svg" - -class drawing: - """d=drawing() - - this is the actual SVG document. It needs a svg element as a root. - Use the addSVG method to set the svg to the root. Use the toXml method to write the SVG - source to the screen or to a file - d=drawing() - d.addSVG(svg) - d.toXml(optionalfilename) - """ - - def __init__(self, entity={}): - self.svg=None - self.entity = entity - def setSVG(self,svg): - self.svg=svg - #Voeg een element toe aan de grafiek toe. - if use_dom_implementation==0: - def toXml(self, filename='',compress=False): - import cStringIO - xml=cStringIO.StringIO() - xml.write("<?xml version='1.0' encoding='UTF-8'?>\n") - xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"") - if self.entity: - xml.write(" [\n") - for item in self.entity.keys(): - xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item])) - xml.write("]") - xml.write(">\n") - self.svg.toXml(0,xml) - if not filename: - if compress: - import gzip - f=cStringIO.StringIO() - zf=gzip.GzipFile(fileobj=f,mode='wb') - zf.write(xml.getvalue()) - zf.close() - f.seek(0) - return f.read() - else: - return xml.getvalue() - else: - if filename[-4:]=='svgz': - import gzip - f=gzip.GzipFile(filename=filename,mode="wb", compresslevel=9) - f.write(xml.getvalue()) - f.close() - else: - f=file(filename,'w') - f.write(xml.getvalue()) - f.close() - - else: - def toXml(self,filename='',compress=False): - """drawing.toXml() ---->to the screen - drawing.toXml(filename)---->to the file - writes a svg drawing to the screen or to a file - compresses if filename ends with svgz or if compress is true - """ - doctype = implementation.createDocumentType('svg',"-//W3C//DTD SVG 1.0//EN""",'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ') - - global root - #root is defined global so it can be used by the appender. Its also possible to use it as an arugument but - #that is a bit messy. - root=implementation.createDocument(None,None,doctype) - #Create the xml document. - global appender - def appender(element,elementroot): - """This recursive function appends elements to an element and sets the attributes - and type. It stops when alle elements have been appended""" - if element.namespace: - e=root.createElementNS(element.namespace,element.type) - else: - e=root.createElement(element.type) - if element.text: - textnode=root.createTextNode(element.text) - e.appendChild(textnode) - for attribute in element.attributes.keys(): #in element.attributes is supported from python 2.2 - e.setAttribute(attribute,str(element.attributes[attribute])) - if element.elements: - for el in element.elements: - e=appender(el,e) - elementroot.appendChild(e) - return elementroot - root=appender(self.svg,root) - if not filename: - import cStringIO - xml=cStringIO.StringIO() - PrettyPrint(root,xml) - if compress: - import gzip - f=cStringIO.StringIO() - zf=gzip.GzipFile(fileobj=f,mode='wb') - zf.write(xml.getvalue()) - zf.close() - f.seek(0) - return f.read() - else: - return xml.getvalue() - else: - try: - if filename[-4:]=='svgz': - import gzip - import cStringIO - xml=cStringIO.StringIO() - PrettyPrint(root,xml) - f=gzip.GzipFile(filename=filename,mode='wb',compresslevel=9) - f.write(xml.getvalue()) - f.close() - else: - f=open(filename,'w') - PrettyPrint(root,f) - f.close() - except: - print "Cannot write SVG file: " + filename - def validate(self): - try: - import xml.parsers.xmlproc.xmlval - except: - raise exceptions.ImportError,'PyXml is required for validating SVG' - svg=self.toXml() - xv=xml.parsers.xmlproc.xmlval.XMLValidator() - try: - xv.feed(svg) - except: - raise "SVG is not well formed, see messages above" - else: - print "SVG well formed" -if __name__=='__main__': - - - d=drawing() - s=svg((0,0,100,100)) - r=rect(-100,-100,300,300,'cyan') - s.addElement(r) - - t=title('SVGdraw Demo') - s.addElement(t) - g=group('animations') - e=ellipse(0,0,5,2) - g.addElement(e) - c=circle(0,0,1,'red') - g.addElement(c) - pd=pathdata(0,-10) - for i in range(6): - pd.relsmbezier(10,5,0,10) - pd.relsmbezier(-10,5,0,10) - an=animateMotion(pd,10) - an.attributes['rotate']='auto-reverse' - an.attributes['repeatCount']="indefinite" - g.addElement(an) - s.addElement(g) - for i in range(20,120,20): - u=use('#animations',i,0) - s.addElement(u) - for i in range(0,120,20): - for j in range(5,105,10): - c=circle(i,j,1,'red','black',.5) - s.addElement(c) - d.setSVG(s) - - print d.toXml() - diff --git a/web/webqtl/utility/webqtlUtil.py b/web/webqtl/utility/webqtlUtil.py deleted file mode 100755 index 6af7f846..00000000 --- a/web/webqtl/utility/webqtlUtil.py +++ /dev/null @@ -1,977 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -import string -import time -import re -import math -from math import * - -from htmlgen import HTMLgen2 as HT - -from base import webqtlConfig - - - - -# NL, 07/27/2010. moved from webqtlForm.py -#Dict of Parents and F1 information, In the order of [F1, Mat, Pat] -ParInfo ={ -'BXH':['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'], -'AKXD':['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'], -'BXD':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'], -'BHHBF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'], -'BHF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'], -'B6D2F2':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'BDF2-1999':['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'], -'BDF2-2005':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'CTB6F2':['CTB6F2','B6CTF2','C57BL/6J','Castaneous'], -'CXB':['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'], -'AXBXA':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], -'AXB':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], -'BXA':['BAF1', 'ABF1', 'C57BL/6J', 'A/J'], -'LXS':['LSF1', 'SLF1', 'ISS', 'ILS'], -'HXBBXH':['HSRBNF1', 'BNHSRF1', 'BN', 'HSR'], -'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0','Shahdara'], -'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0','Bur-0'], -'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0','Cvi'], -'SXM':['SMF1', 'MSF1', 'Steptoe','Morex'] -} - - -# NL, 07/27/2010. moved from template.py -IMGSTEP1 = HT.Image('/images/step1.gif', alt='STEP 1',border=0) #XZ, Only be used in inputPage.py -IMGSTEP2 = HT.Image('/images/step2.gif', alt='STEP 2',border=0) #XZ, Only be used in inputPage.py -IMGSTEP3 = HT.Image('/images/step3.gif', alt='STEP 3',border=0) #XZ, Only be used in inputPage.py -IMGNEXT = HT.Image('/images/arrowdown.gif', alt='NEXT',border=0) #XZ, Only be used in inputPage.py - -IMGASC = HT.Image("/images/sortup.gif", border=0) -IMGASCON = HT.Image("/images/sortupon.gif", border=0) -IMGDESC = HT.Image("/images/sortdown.gif", border=0) -IMGDESCON = HT.Image("/images/sortdownon.gif", border=0) - -""" -IMGASC = HT.Image("/images/sortup_icon.gif", border=0) -IMGASCON = HT.Image("/images/sortupon.gif", border=0) -IMGDESC = HT.Image("/images/sortdown_icon.gif", border=0) -IMGDESCON = HT.Image("/images/sortdownon.gif", border=0) -IMG_UNSORTED = HT.Image("/images/unsorted_icon.gif", border=0) -""" - -PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle",border=0) - -######################################### -# Accessory Functions -######################################### - -def decodeEscape(str): - a = str - pattern = re.compile('(%[0-9A-Fa-f][0-9A-Fa-f])') - match = pattern.findall(a) - matched = [] - for item in match: - if item not in matched: - a = a.replace(item, '%c' % eval("0x"+item[-2:])) - matched.append(item) - return a - -def exportData(hddn, tdata, NP = None): - for key in tdata.keys(): - _val, _var, _N = tdata[key].val, tdata[key].var, tdata[key].N - if _val != None: - hddn[key] = _val - if _var != None: - hddn['V'+key] = _var - if NP and _N != None: - hddn['N'+key] = _N - -def genShortStrainName(RISet='', input_strainName=''): - #aliasStrainDict = {'C57BL/6J':'B6','DBA/2J':'D2'} - strainName = input_strainName - if RISet != 'AXBXA': - if RISet == 'BXD300': - this_RISet = 'BXD' - elif RISet == 'BDF2-2005': - this_RISet = 'CASE05_' - else: - this_RISet = RISet - strainName = string.replace(strainName,this_RISet,'') - strainName = string.replace(strainName,'CASE','') - try: - strainName = "%02d" % int(strainName) - except: - pass - else: - strainName = string.replace(strainName,'AXB','A') - strainName = string.replace(strainName,'BXA','B') - try: - strainName = strainName[0] + "%02d" % int(strainName[1:]) - except: - pass - return strainName - -def toInt(in_str): - "Converts an arbitrary string to an unsigned integer" - start = -1 - end = -1 - for i, char in enumerate(in_str): - if char >= '0' and char <= '9': - if start < 0: - start = i - end = i+1 - else: - if start >= 0: - break - if start < end: - return int(in_str[start:end]) - else: - return -1 - -def transpose(m): - 'transpose a matrix' - n = len(m) - return [[m[j][i] for i in range(len(m[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m[0]))] - -def asymTranspose(m): - 'transpose a matrix' - t = max(map(len, m)) - n = len(m) - m2 = [["-"]]*n - for i in range(n): - m2[i] = m[i] + [""]*(t- len(m[i])) - return [[m2[j][i] for i in range(len(m2[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m2[0]))] - -def genRandStr(prefix = "", length=8, chars=string.letters+string.digits): - from random import choice - _str = prefix[:] - for i in range(length): - _str += choice(chars) - return _str - -def generate_session(): - import sha - return sha.new(str(time.time())).hexdigest() - -def cvt2Dict(x): - tmp = {} - for key in x.keys(): - tmp[key] = x[key] - return tmp - -def dump_session(session_obj, filename): - "It seems mod python can only cPickle most basic data type" - import cPickle - session_file = open(filename, 'wb') - #try: - # pass - #except: - # pass - cPickle.dump(session_obj, session_file) - session_file.close() - -def StringAsFloat(str): - 'Converts string to float but catches any exception and returns None' - try: - return float(str) - except: - return None - -def IntAsFloat(str): - 'Converts string to Int but catches any exception and returns None' - try: - return int(str) - except: - return None - -def FloatAsFloat(flt): - 'Converts float to string but catches any exception and returns None' - try: - return float("%2.3f" % flt) - except: - return None - -def RemoveZero(flt): - 'Converts string to float but catches any exception and returns None' - try: - if abs(flt) < 1e-6: - return None - else: - return flt - except: - return None - - -def SciFloat(d): - 'Converts string to float but catches any exception and returns None' - - try: - if abs(d) <= 1.0e-4: - return "%1.2e" % d - else: - return "%1.5f" % d - except: - return None - -###To be removed -def FloatList2String(lst): - 'Converts float list to string but catches any exception and returns None' - tt='' - try: - for item in lst: - if item == None: - tt += 'X ' - else: - tt += '%f ' % item - return tt - except: - return "" - -def ListNotNull(lst): - 'Determine if the elements in a list are all null' - for item in lst: - if item is not None: - return 1 - return None - -###To be removed -def FileDataProcess(str): - 'Remove the description text from the input file if theres any' - i=0 - while i<len(str): - if str[i]<'\x7f' and str[i]>'\x20': - break - else: - i+=1 - str=str[i:] - str=string.join(string.split(str,'\000'),'') - i=string.find(str,"*****") - if i>-1: - return str[i+5:] - else: - return str - -def rank(a,lst,offset=0): - """Calculate the integer rank of a number in an array, can be used to calculate p-value""" - n = len(lst) - if n == 2: - if a <lst[0]: - return offset - elif a > lst[1]: - return offset + 2 - else: - return offset +1 - elif n == 1: - if a <lst[0]: - return offset - else: - return offset +1 - elif n== 0: - return offset - else: - mid = n/2 - if a < lst[mid]: - return rank(a,lst[:mid-1],offset) - else: - return rank(a,lst[mid:],offset+mid) - -def cmpScanResult(A,B): - try: - if A.LRS > B.LRS: - return 1 - elif A.LRS == B.LRS: - return 0 - else: - return -1 - except: - return 0 - - -def cmpScanResult2(A,B): - try: - if A.LRS < B.LRS: - return 1 - elif A.LRS == B.LRS: - return 0 - else: - return -1 - except: - return 0 - -def cmpOrder(A,B): - try: - if A[1] < B[1]: - return -1 - elif A[1] == B[1]: - return 0 - else: - return 1 - except: - return 0 - -def cmpOrder2(A,B): - try: - if A[-1] < B[-1]: - return -1 - elif A[-1] == B[-1]: - return 0 - else: - return 1 - except: - return 0 - - - - -def calRank(xVals, yVals, N): ### Zach Sloan, February 4 2010 - """ - Returns a ranked set of X and Y values. These are used when generating - a Spearman scatterplot. Bear in mind that this sets values equal to each - other as the same rank. - """ - XX = [] - YY = [] - X = [0]*len(xVals) - Y = [0]*len(yVals) - j = 0 - - for i in range(len(xVals)): - - if xVals[i] != None and yVals[i] != None: - XX.append((j, xVals[i])) - YY.append((j, yVals[i])) - j = j + 1 - - NN = len(XX) - - XX.sort(cmpOrder2) - YY.sort(cmpOrder2) - - j = 1 - rank = 0.0 - - while j < NN: - - if XX[j][1] != XX[j-1][1]: - X[XX[j-1][0]] = j - j = j+1 - - else: - jt = j+1 - ji = j - for jt in range(j+1, NN): - if (XX[jt][1] != XX[j-1][1]): - break - rank = 0.5*(j+jt) - for ji in range(j-1, jt): - X[XX[ji][0]] = rank - if (jt == NN-1): - if (XX[jt][1] == XX[j-1][1]): - X[XX[NN-1][0]] = rank - j = jt+1 - - if j == NN: - if X[XX[NN-1][0]] == 0: - X[XX[NN-1][0]] = NN - - j = 1 - rank = 0.0 - - while j < NN: - - if YY[j][1] != YY[j-1][1]: - Y[YY[j-1][0]] = j - j = j+1 - else: - jt = j+1 - ji = j - for jt in range(j+1, NN): - if (YY[jt][1] != YY[j-1][1]): - break - rank = 0.5*(j+jt) - for ji in range(j-1, jt): - Y[YY[ji][0]] = rank - if (jt == NN-1): - if (YY[jt][1] == YY[j-1][1]): - Y[YY[NN-1][0]] = rank - j = jt+1 - - if j == NN: - if Y[YY[NN-1][0]] == 0: - Y[YY[NN-1][0]] = NN - - return (X,Y) - -def calCorrelationRank(xVals,yVals,N): - """ - Calculated Spearman Ranked Correlation. The algorithm works - by setting all tied ranks to the average of those ranks (for - example, if ranks 5-10 all have the same value, each will be set - to rank 7.5). - """ - - XX = [] - YY = [] - j = 0 - - for i in range(len(xVals)): - if xVals[i]!= None and yVals[i]!= None: - XX.append((j,xVals[i])) - YY.append((j,yVals[i])) - j = j+1 - - NN = len(XX) - if NN <6: - return (0.0,NN) - XX.sort(cmpOrder2) - YY.sort(cmpOrder2) - X = [0]*NN - Y = [0]*NN - - j = 1 - rank = 0.0 - t = 0.0 - sx = 0.0 - - while j < NN: - - if XX[j][1] != XX[j-1][1]: - X[XX[j-1][0]] = j - j = j+1 - - else: - jt = j+1 - ji = j - for jt in range(j+1, NN): - if (XX[jt][1] != XX[j-1][1]): - break - rank = 0.5*(j+jt) - for ji in range(j-1, jt): - X[XX[ji][0]] = rank - t = jt-j - sx = sx + (t*t*t-t) - if (jt == NN-1): - if (XX[jt][1] == XX[j-1][1]): - X[XX[NN-1][0]] = rank - j = jt+1 - - if j == NN: - if X[XX[NN-1][0]] == 0: - X[XX[NN-1][0]] = NN - - j = 1 - rank = 0.0 - t = 0.0 - sy = 0.0 - - while j < NN: - - if YY[j][1] != YY[j-1][1]: - Y[YY[j-1][0]] = j - j = j+1 - else: - jt = j+1 - ji = j - for jt in range(j+1, NN): - if (YY[jt][1] != YY[j-1][1]): - break - rank = 0.5*(j+jt) - for ji in range(j-1, jt): - Y[YY[ji][0]] = rank - t = jt - j - sy = sy + (t*t*t-t) - if (jt == NN-1): - if (YY[jt][1] == YY[j-1][1]): - Y[YY[NN-1][0]] = rank - j = jt+1 - - if j == NN: - if Y[YY[NN-1][0]] == 0: - Y[YY[NN-1][0]] = NN - - D = 0.0 - - for i in range(NN): - D += (X[i]-Y[i])*(X[i]-Y[i]) - - fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN)) - - return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN) - - -def calCorrelationRankText(dbdata,userdata,N): ### dcrowell = David Crowell, July 2008 - """Calculates correlation ranks with data formatted from the text file. - dbdata, userdata are lists of strings. N is an int. Returns a float. - Used by correlationPage""" - XX = [] - YY = [] - j = 0 - for i in range(N): - if (dbdata[i]!= None and userdata[i]!=None) and (dbdata[i]!= 'None' and userdata[i]!='None'): - XX.append((j,float(dbdata[i]))) - YY.append((j,float(userdata[i]))) - j += 1 - NN = len(XX) - if NN <6: - return (0.0,NN) - XX.sort(cmpOrder2) - YY.sort(cmpOrder2) - X = [0]*NN - Y = [0]*NN - - j = 1 - rank = 0.0 - t = 0.0 - sx = 0.0 - - while j < NN: - - if XX[j][1] != XX[j-1][1]: - X[XX[j-1][0]] = j - j = j+1 - - else: - jt = j+1 - ji = j - for jt in range(j+1, NN): - if (XX[jt][1] != XX[j-1][1]): - break - rank = 0.5*(j+jt) - for ji in range(j-1, jt): - X[XX[ji][0]] = rank - t = jt-j - sx = sx + (t*t*t-t) - if (jt == NN-1): - if (XX[jt][1] == XX[j-1][1]): - X[XX[NN-1][0]] = rank - j = jt+1 - - if j == NN: - if X[XX[NN-1][0]] == 0: - X[XX[NN-1][0]] = NN - - j = 1 - rank = 0.0 - t = 0.0 - sy = 0.0 - - while j < NN: - - if YY[j][1] != YY[j-1][1]: - Y[YY[j-1][0]] = j - j = j+1 - else: - jt = j+1 - ji = j - for jt in range(j+1, NN): - if (YY[jt][1] != YY[j-1][1]): - break - rank = 0.5*(j+jt) - for ji in range(j-1, jt): - Y[YY[ji][0]] = rank - t = jt - j - sy = sy + (t*t*t-t) - if (jt == NN-1): - if (YY[jt][1] == YY[j-1][1]): - Y[YY[NN-1][0]] = rank - j = jt+1 - - if j == NN: - if Y[YY[NN-1][0]] == 0: - Y[YY[NN-1][0]] = NN - - D = 0.0 - - for i in range(NN): - D += (X[i]-Y[i])*(X[i]-Y[i]) - - fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN)) - - return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN) - - - -def calCorrelation(dbdata,userdata,N): - X = [] - Y = [] - for i in range(N): - if dbdata[i]!= None and userdata[i]!= None: - X.append(dbdata[i]) - Y.append(userdata[i]) - NN = len(X) - if NN <6: - return (0.0,NN) - sx = reduce(lambda x,y:x+y,X,0.0) - sy = reduce(lambda x,y:x+y,Y,0.0) - meanx = sx/NN - meany = sy/NN - xyd = 0.0 - sxd = 0.0 - syd = 0.0 - for i in range(NN): - xyd += (X[i] - meanx)*(Y[i]-meany) - sxd += (X[i] - meanx)*(X[i] - meanx) - syd += (Y[i] - meany)*(Y[i] - meany) - try: - corr = xyd/(sqrt(sxd)*sqrt(syd)) - except: - corr = 0 - return (corr,NN) - -def calCorrelationText(dbdata,userdata,N): ### dcrowell July 2008 - """Calculates correlation coefficients with values formatted from text files. dbdata, userdata are lists of strings. N is an int. Returns a float - Used by correlationPage""" - X = [] - Y = [] - for i in range(N): - #if (dbdata[i]!= None and userdata[i]!= None) and (dbdata[i]!= 'None' and userdata[i]!= 'None'): - # X.append(float(dbdata[i])) - # Y.append(float(userdata[i])) - if dbdata[i] == None or dbdata[i] == 'None' or userdata[i] == None or userdata[i] == 'None': - continue - else: - X.append(float(dbdata[i])) - Y.append(float(userdata[i])) - NN = len(X) - if NN <6: - return (0.0,NN) - sx = sum(X) - sy = sum(Y) - meanx = sx/float(NN) - meany = sy/float(NN) - xyd = 0.0 - sxd = 0.0 - syd = 0.0 - for i in range(NN): - x1 = X[i]-meanx - y1 = Y[i]-meany - xyd += x1*y1 - sxd += x1**2 - syd += y1**2 - try: - corr = xyd/(sqrt(sxd)*sqrt(syd)) - except: - corr = 0 - return (corr,NN) - - -def readLineCSV(line): ### dcrowell July 2008 - """Parses a CSV string of text and returns a list containing each element as a string. - Used by correlationPage""" - returnList = line.split('","') - returnList[-1]=returnList[-1][:-2] - returnList[0]=returnList[0][1:] - return returnList - - -def cmpCorr(A,B): - try: - if abs(A[1]) < abs(B[1]): - return 1 - elif abs(A[1]) == abs(B[1]): - return 0 - else: - return -1 - except: - return 0 - -def cmpLitCorr(A,B): - try: - if abs(A[3]) < abs(B[3]): return 1 - elif abs(A[3]) == abs(B[3]): - if abs(A[1]) < abs(B[1]): return 1 - elif abs(A[1]) == abs(B[1]): return 0 - else: return -1 - else: return -1 - except: - return 0 - -def cmpPValue(A,B): - try: - if A.corrPValue < B.corrPValue: - return -1 - elif A.corrPValue == B.corrPValue: - if abs(A.corr) > abs(B.corr): - return -1 - elif abs(A.corr) < abs(B.corr): - return 1 - else: - return 0 - else: - return 1 - except: - return 0 - -def cmpEigenValue(A,B): - try: - if A[0] > B[0]: - return -1 - elif A[0] == B[0]: - return 0 - else: - return 1 - except: - return 0 - - -def cmpLRSFull(A,B): - try: - if A[0] < B[0]: - return -1 - elif A[0] == B[0]: - return 0 - else: - return 1 - except: - return 0 - -def cmpLRSInteract(A,B): - try: - if A[1] < B[1]: - return -1 - elif A[1] == B[1]: - return 0 - else: - return 1 - except: - return 0 - - -def cmpPos(A,B): - try: - try: - AChr = int(A.chr) - except: - AChr = 20 - try: - BChr = int(B.chr) - except: - BChr = 20 - if AChr > BChr: - return 1 - elif AChr == BChr: - if A.mb > B.mb: - return 1 - if A.mb == B.mb: - return 0 - else: - return -1 - else: - return -1 - except: - return 0 - -def cmpGenoPos(A,B): - try: - A1 = A.chr - B1 = B.chr - try: - A1 = int(A1) - except: - A1 = 25 - try: - B1 = int(B1) - except: - B1 = 25 - if A1 > B1: - return 1 - elif A1 == B1: - if A.mb > B.mb: - return 1 - if A.mb == B.mb: - return 0 - else: - return -1 - else: - return -1 - except: - return 0 - -#XZhou: Must use "BINARY" to enable case sensitive comparison. -def authUser(name,password,db, encrypt=None): - try: - if encrypt: - query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY \'%s\'' % (name,password) - else: - query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY SHA(\'%s\')' % (name,password) - db.execute(query) - records = db.fetchone() - if not records: - raise ValueError - return records#(privilege,id,name,password,grpName) - except: - return (None, None, None, None, None) - - -def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users): - access_to_confidential_phenotype_trait = 0 - if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']: - access_to_confidential_phenotype_trait = 1 - else: - AuthorizedUsersList=map(string.strip, string.split(authorized_users, ',')) - if AuthorizedUsersList.__contains__(userName): - access_to_confidential_phenotype_trait = 1 - return access_to_confidential_phenotype_trait - - -class VisualizeException(Exception): - def __init__(self, message): - self.message = message - def __str__(self): - return self.message - -# safeConvert : (string -> A) -> A -> A -# to convert a string to type A, using the supplied default value -# if the given conversion function doesn't work -def safeConvert(f, value, default): - try: - return f(value) - except: - return default - -# safeFloat : string -> float -> float -# to convert a string to a float safely -def safeFloat(value, default): - return safeConvert(float, value, default) - -# safeInt: string -> int -> int -# to convert a string to an int safely -def safeInt(value, default): - return safeConvert(int, value, default) - -# safeString : string -> (arrayof string) -> string -> string -# if a string is not in a list of strings to pick a default value -# for that string -def safeString(value, validChoices, default): - if value in validChoices: - return value - else: - return default - -# yesNoToInt: string -> int -# map "yes" -> 1 and "no" -> 0 -def yesNoToInt(value): - if value == "yes": - return 1 - elif value == "no": - return 0 - else: - return None - -# IntToYesNo: int -> string -# map 1 -> "yes" and 0 -> "no" -def intToYesNo(value): - if value == 1: - return "yes" - elif value == 0: - return "no" - else: - return None - -def formatField(name): - name = name.replace("_", " ") - name = name.title() - #name = name.replace("Mb Mm6", "Mb"); - return name.replace("Id", "ID") - -#XZ, 03/27/2009: This function is very specific. -#It is used by AJAX_table.py, correlationPage.py and dataPage.py - - -def genTableObj(tblobj=None, file="", sortby = ("", ""), tableID = "sortable", addIndex = "1", hiddenColumns=[]): - header = tblobj['header'] - body = tblobj['body'] - field, order = sortby - - #ZAS 9/12/2011 - The hiddenColumns array needs to be converted into a string so they can be placed into the javascript of each up/down button - hiddenColumnsString = ",".join(hiddenColumns) - - tbl = HT.TableLite(Class="collap b2", cellspacing=1, cellpadding=5) - - hiddenColumnIdx = [] #indices of columns to hide - idx = -1 - last_idx = 0 #ZS: This is the index of the last item in the regular table header (without any extra parameters). It is used to determine the index of each extra parameter. - for row in header: - hr = HT.TR() - for i, item in enumerate(row): - if (item.text == '') or (item.text not in hiddenColumns): - if item.sort and item.text: - down = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=down&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGDESC) - up = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=up&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGASC) - if item.text == field: - idx = item.idx - last_idx = idx - if order == 'up': - up = IMGASCON - elif order == 'down': - down = IMGDESCON - item.html.append(HT.Div(up, down, style="float: bottom;")) - hr.append(item.html) - else: - hiddenColumnIdx.append(i) - tbl.append(hr) - - for i, row in enumerate(body): - for j, item in enumerate(row): - if order == 'down': - if (item.val == '' or item.val == 'x' or item.val == 'None'): - item.val = 0 - if order == 'up': - if (item.val == '' or item.val == 'x' or item.val == 'None'): - item.val = 'zzzzz' - - if idx >= 0: - if order == 'down': - body.sort(lambda A, B: cmp(B[idx].val, A[idx].val), key=natsort_key) - elif order == 'up': - body.sort(lambda A, B: cmp(A[idx].val, B[idx].val), key=natsort_key) - else: - pass - - for i, row in enumerate(body): - hr = HT.TR(Id = row[0].text) - for j, item in enumerate(row): - if (j not in hiddenColumnIdx): - if j == 0: - if addIndex == "1": - item.html.contents = [i+1] + item.html.contents - hr.append(item.html) - tbl.append(hr) - - return tbl - -def natsort_key(string): - r = [] - for c in string: - try: - c = int(c) - try: r[-1] = r[-1] * 10 + c - except: r.append(c) - except: - r.append(c) - return r - |