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, 3568 insertions, 0 deletions
diff --git a/web/webqtl/utility/AJAX_table.py b/web/webqtl/utility/AJAX_table.py new file mode 100755 index 00000000..963a530e --- /dev/null +++ b/web/webqtl/utility/AJAX_table.py @@ -0,0 +1,153 @@ +# 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 new file mode 100755 index 00000000..2401c85c --- /dev/null +++ b/web/webqtl/utility/Plot.py @@ -0,0 +1,1283 @@ +# 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 new file mode 100755 index 00000000..76b9c5db --- /dev/null +++ b/web/webqtl/utility/TDCell.py @@ -0,0 +1,42 @@ +# 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 new file mode 100755 index 00000000..a96b9e49 --- /dev/null +++ b/web/webqtl/utility/THCell.py @@ -0,0 +1,44 @@ +# 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 new file mode 100755 index 00000000..e69de29b --- /dev/null +++ b/web/webqtl/utility/__init__.py diff --git a/web/webqtl/utility/svg.py b/web/webqtl/utility/svg.py new file mode 100755 index 00000000..e49a6c3c --- /dev/null +++ b/web/webqtl/utility/svg.py @@ -0,0 +1,1069 @@ +# 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 new file mode 100755 index 00000000..6af7f846 --- /dev/null +++ b/web/webqtl/utility/webqtlUtil.py @@ -0,0 +1,977 @@ +# 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 + |