From 527bb0459cf488e5021696e326dc10d28ecdd74c Mon Sep 17 00:00:00 2001 From: Sam Ockman Date: Thu, 24 May 2012 02:18:20 -0400 Subject: Trying to get stuff working under new structure --- wqflask/utility/AJAX_table.py | 153 +++++ wqflask/utility/Plot.py | 1283 +++++++++++++++++++++++++++++++++++++++++ wqflask/utility/TDCell.py | 42 ++ wqflask/utility/THCell.py | 44 ++ wqflask/utility/__init__.py | 0 wqflask/utility/formatting.py | 109 ++++ wqflask/utility/svg.py | 1069 ++++++++++++++++++++++++++++++++++ wqflask/utility/webqtlUtil.py | 977 +++++++++++++++++++++++++++++++ 8 files changed, 3677 insertions(+) create mode 100755 wqflask/utility/AJAX_table.py create mode 100755 wqflask/utility/Plot.py create mode 100755 wqflask/utility/TDCell.py create mode 100755 wqflask/utility/THCell.py create mode 100755 wqflask/utility/__init__.py create mode 100644 wqflask/utility/formatting.py create mode 100755 wqflask/utility/svg.py create mode 100755 wqflask/utility/webqtlUtil.py (limited to 'wqflask/utility') diff --git a/wqflask/utility/AJAX_table.py b/wqflask/utility/AJAX_table.py new file mode 100755 index 00000000..963a530e --- /dev/null +++ b/wqflask/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 = "The table is no longer available on this server" + + def __str__(self): + return self.value + + def write(self): + return str(self) diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py new file mode 100755 index 00000000..2401c85c --- /dev/null +++ b/wqflask/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)=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/wqflask/utility/TDCell.py b/wqflask/utility/TDCell.py new file mode 100755 index 00000000..76b9c5db --- /dev/null +++ b/wqflask/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/wqflask/utility/THCell.py b/wqflask/utility/THCell.py new file mode 100755 index 00000000..a96b9e49 --- /dev/null +++ b/wqflask/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/wqflask/utility/__init__.py b/wqflask/utility/__init__.py new file mode 100755 index 00000000..e69de29b diff --git a/wqflask/utility/formatting.py b/wqflask/utility/formatting.py new file mode 100644 index 00000000..52173417 --- /dev/null +++ b/wqflask/utility/formatting.py @@ -0,0 +1,109 @@ +def numify(number, singular=None, plural=None): + """Turn a number into a word if less than 13 and optionally add a singular or plural word + + >>> numify(3) + 'three' + + >>> numify(1, 'item', 'items') + 'one item' + + >>> numify(9, 'book', 'books') + 'nine books' + + >>> numify(15) + '15' + + >>> numify(0) + '0' + + >>> numify(12334, 'hippopotamus', 'hippopotami') + '12,334 hippopotami' + + """ + num_repr = {1 : "one", + 2 : "two", + 3 : "three", + 4 : "four", + 5 : "five", + 6 : "six", + 7 : "seven", + 8 : "eight", + 9 : "nine", + 10 : "ten", + 11 : "eleven", + 12 : "twelve"} + + #Below line commented out cause doesn't work in Python 2.4 + #assert all((singular, plural)) or not any((singular, plural)), "Need to pass two words or none" + if number == 1: + word = singular + else: + word = plural + + if number in num_repr: + number = num_repr[number] + elif number > 9999: + number = commify(number) + + if word: + return "%s %s" % (number, word) + else: + return str(number) + + +def commify(n): + """Add commas to an integer n. + + See http://stackoverflow.com/questions/3909457/whats-the-easiest-way-to-add-commas-to-an-integer-in-python + But I (Sam) made some small changes based on http://www.grammarbook.com/numbers/numbers.asp + + >>> commify(1) + '1' + >>> commify(123) + '123' + >>> commify(1234) + '1234' + >>> commify(12345) + '12,345' + >>> commify(1234567890) + '1,234,567,890' + >>> commify(123.0) + '123.0' + >>> commify(1234.5) + '1234.5' + >>> commify(1234.56789) + '1234.56789' + >>> commify(123456.789) + '123,456.789' + >>> commify('%.2f' % 1234.5) + '1234.50' + >>> commify(None) + >>> + + """ + if n is None: + return None + + n = str(n) + + if len(n) <= 4: # Might as well do this early + return n + + if '.' in n: + dollars, cents = n.split('.') + else: + dollars, cents = n, None + + # Don't commify numbers less than 10000 + if len(dollars) <= 4: + return n + + r = [] + for i, c in enumerate(reversed(str(dollars))): + if i and (not (i % 3)): + r.insert(0, ',') + r.insert(0, c) + out = ''.join(r) + if cents: + out += '.' + cents + return out diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py new file mode 100755 index 00000000..e49a6c3c --- /dev/null +++ b/wqflask/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 text 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 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)+'\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+'\n') + elif self.text: + f.write('\n') + elif self.cdata: + f.write('\t'*level+'\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="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("\n") + xml.write("\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/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py new file mode 100755 index 00000000..6af7f846 --- /dev/null +++ b/wqflask/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'\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[1]: + return offset + 2 + else: + return offset +1 + elif n == 1: + if a 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 + -- cgit 1.4.1 From 93fdf06d57770c985e0ca8169977c210a891e262 Mon Sep 17 00:00:00 2001 From: Sam Ockman Date: Sat, 2 Jun 2012 04:43:31 -0400 Subject: Coming along in trying to get trait page working --- wqflask/utility/Plot.py | 334 +++++++++++++------------- wqflask/wqflask/show_trait/show_trait_page.py | 40 ++- wqflask/wqflask/views.py | 2 + 3 files changed, 188 insertions(+), 188 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 2401c85c..e00b8e9e 100755 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -24,7 +24,7 @@ # # Last updated by GeneNetwork Core Team 2010/10/20 -import piddle as pid +#import piddle as pid from math import * import random import sys, os @@ -41,7 +41,7 @@ from base import webqtlConfig def cformat(d, rank=0): 'custom string format' strD = "%2.6f" % d - + if rank == 0: while strD[-1] in ('0','.'): if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4: @@ -51,29 +51,29 @@ def cformat(d, rank=0): break else: strD = strD[:-1] - + else: - strD = strD.split(".")[0] + strD = strD.split(".")[0] if strD == '-0.0': strD = '0.0' return strD - -def frange(start, end=None, inc=1.0): - "A faster range-like function that does accept float increments..." - if end == None: - end = start + 0.0 - start = 0.0 - else: - start += 0.0 # force it to be a float - count = int((end - start) / inc) - if start + count * inc != end: - # Need to adjust the count. AFAICT, it always comes up one short. - count += 1 - L = [start] * count - for i in xrange(1, count): - L[i] = start + i * inc - return L + +def frange(start, end=None, inc=1.0): + "A faster range-like function that does accept float increments..." + if end == None: + end = start + 0.0 + start = 0.0 + else: + start += 0.0 # force it to be a float + count = int((end - start) / inc) + if start + count * inc != end: + # Need to adjust the count. AFAICT, it always comes up one short. + count += 1 + L = [start] * count + for i in xrange(1, count): + L[i] = start + i * inc + return L def gammln(xx): @@ -85,15 +85,15 @@ def gammln(xx): for item in cof: x+=1.0 ser+=item/x - + return -tmp+log(2.50662827465*ser) - + def gser(a,x): gln=gammln(a) ITMAX=100 EPS=3.0e-7 - + if x<=0.0: gamser=0.0 return [gamser,gln] @@ -109,7 +109,7 @@ def gser(a,x): gamser=sum*exp(-x+a*log(x)-gln) return [gamser,gln] return None - + def gcf(a,x): ITMAX=100 EPS=3.0e-7 @@ -119,7 +119,7 @@ def gcf(a,x): b0=0.0 a0=1.0 gln=gammln(a) - + a1=x for n in range(1,ITMAX+1): an=n+0.0 @@ -137,7 +137,7 @@ def gcf(a,x): return [gammcf,gln] gold=g return None - + def gammp(a,x): if x<0.0 or a<=0.0: return None @@ -155,7 +155,7 @@ def U(n): m.append(a) m.append(x) return m - + def erf(x): if x<0.0: return -gammp(0.5,x*x) @@ -170,7 +170,7 @@ def erfcc(x): return ans else: return 2.0-ans - + def calMeanVar(data): n=len(data) if n<2: @@ -187,7 +187,7 @@ def calMeanVar(data): for i in range(n): z[i]=z[i]/variance return z - + def inverseCumul(p): #Coefficients in rational approximations. a = [-3.969683028665376e+01,2.209460984245205e+02,-2.759285104469687e+02,1.383577518672690e+02,-3.066479806614716e+01,2.506628277459239e+00] @@ -227,7 +227,7 @@ def inverseCumul(p): return None if p>0 and p < 1: - e = 0.5 * erfcc(-x/sqrt(2)) - p + e = 0.5 * erfcc(-x/sqrt(2)) - p u = e * sqrt(2*pi) * exp(x*x/2) x = x - u/(1 + x*u/2) return x @@ -252,7 +252,7 @@ def gmedian(lst2): return (lst[N/2]+lst[(N-2)/2])/2.0 else: return lst[(N-1)/2] - + def gpercentile(lst2, np): lst = lst2[:] N = len(lst) @@ -269,21 +269,21 @@ def gpercentile(lst2, np): return lst[N-1] else: return lst[k-1] + d*(lst[k] - lst[k-1]) - + def findOutliers(vals): - + valsOnly = [] dataXZ = vals[:] for i in range(len(dataXZ)): valsOnly.append(dataXZ[i][1]) - - data = [('', valsOnly[:])] - + + data = [('', valsOnly[:])] + for item in data: itemvalue = item[1] nValue = len(itemvalue) catValue = [] - + for item2 in itemvalue: try: tstrain, tvalue = item2 @@ -293,18 +293,18 @@ def findOutliers(vals): continue else: catValue.append(tvalue) - + if catValue != []: lowHinge = gpercentile(catValue, 25) upHinge = gpercentile(catValue, 75) Hstep = 1.5*(upHinge - lowHinge) - + outlier = [] extreme = [] - + upperBound = upHinge + Hstep lowerBound = lowHinge - Hstep - + for item in catValue: if item >= upHinge + 2*Hstep: extreme.append(item) @@ -312,7 +312,7 @@ def findOutliers(vals): outlier.append(item) else: pass - + for item in catValue: if item <= lowHinge - 2*Hstep: extreme.append(item) @@ -323,10 +323,10 @@ def findOutliers(vals): else: upperBound = 1000 lowerBound = -1000 - + return upperBound, lowerBound - - + + def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabel="Value"): xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset @@ -338,8 +338,8 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe iValues.append(item2[1]) except: iValues.append(item2) - - #draw frame + + #draw frame max_Y = max(iValues) min_Y = min(iValues) scaleY = detScale(min_Y, max_Y) @@ -349,7 +349,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe stepY = (Yur - Yll)/nStep stepYPixel = plotHeight/(nStep) canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset) - + ##draw Y Scale YYY = Yll YCoord = plotHeight + yTopOffset @@ -361,7 +361,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe canvas.drawString(strY, xLeftOffset -30,YCoord +5,font=scaleFont) YYY += stepY YCoord -= stepYPixel - + ##draw X Scale stepX = plotWidth/len(data) XCoord = xLeftOffset + 0.5*stepX @@ -373,7 +373,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe canvas.drawLine(XCoord, YCoord,XCoord, YCoord+5, color=pid.black) canvas.drawString(itemname, XCoord - canvas.stringWidth(itemname,font=labelFont)/2.0,\ YCoord +20,font=labelFont) - + nValue = len(itemvalue) catValue = [] for item2 in itemvalue: @@ -391,10 +391,10 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe lowHinge = gpercentile(catValue, 25) upHinge = gpercentile(catValue, 75) Hstep = 1.5*(upHinge - lowHinge) - + outlier = [] extrem = [] - + upperAdj = None for item in catValue: if item >= upHinge + 2*Hstep: @@ -431,7 +431,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe XCoord, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll)) canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll), \ XCoord+20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll)) - + outlierFont = pid.Font(ttf="cour",size=12,bold=0) if outlier != []: for item in outlier: @@ -443,14 +443,14 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll) #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3) canvas.drawString('*', XCoord-3, yc+6, font=outlierFont, color=pid.red) - + canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \ color=pid.blue,size=3) #print (catMean, catMedian, cat25per, cat75per) pass - + XCoord += stepX - + labelFont=pid.Font(ttf="verdana",size=18,bold=0) canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, \ YCoord +40, font=labelFont) @@ -465,48 +465,48 @@ def plotSecurity(canvas, text="12345"): plotHeight = canvas.size[1] if plotHeight<=0 or plotWidth<=0: return - + bgColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random()) canvas.drawRect(0,0,plotWidth,plotHeight, edgeColor=bgColor, fillColor=bgColor) - + for i in range(30): randomColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random()) scaleFont=pid.Font(ttf="cour",size=random.choice(range(20, 50))) - canvas.drawString(random.choice('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'), - int(random.random()*plotWidth), int(random.random()*plotHeight), font=scaleFont, + canvas.drawString(random.choice('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'), + int(random.random()*plotWidth), int(random.random()*plotHeight), font=scaleFont, color=randomColor, angle=random.choice(range(-45, 50))) - + step = (plotWidth-20)/len(text) startX = 20 for item in text: randomColor = pid.Color(0.6*random.random(),0.6*random.random(), 0.6*random.random()) scaleFont=pid.Font(ttf="verdana",size=random.choice(range(50, 60)),bold=1) - canvas.drawString(item, startX, plotHeight/2-10, font=scaleFont, + canvas.drawString(item, startX, plotHeight/2-10, font=scaleFont, color=randomColor, angle=random.choice(range(-45, 50))) startX += step - + # parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py) -# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py) +# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py) def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1): - + xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset - + plotWidth = canvas.size[0] - xLeftOffset - xRightOffset plotHeight = canvas.size[1] - yTopOffset - yBottomOffset if plotHeight<=0 or plotWidth<=0: return - + if len(data) < 2: return - + max_D = max(data) min_D = min(data) #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong if max_D == float('inf') or max_D>webqtlConfig.MAXLRS: max_D=webqtlConfig.MAXLRS #maximum LRS value - + xLow, xTop, stepX = detScale(min_D, max_D) - + #reduce data step = ceil((xTop-xLow)/50.0) j = xLow @@ -515,27 +515,27 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid while j <= xTop: dataXY.append(j) Count.append(0) - j += step - + j += step + for i, item in enumerate(data): if item == float('inf') or item>webqtlConfig.MAXLRS: item = webqtlConfig.MAXLRS #maximum LRS value j = int((item-xLow)/step) - Count[j] += 1 - + Count[j] += 1 + yLow, yTop, stepY=detScale(0,max(Count)) - + #draw data xScale = plotWidth/(xTop-xLow) yScale = plotHeight/(yTop-yLow) barWidth = xScale*step - + for i, count in enumerate(Count): if count: xc = (dataXY[i]-xLow)*xScale+xLeftOffset yc =-(count-yLow)*yScale+yTopOffset+plotHeight canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor) - + #draw drawing region canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight) @@ -548,7 +548,7 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid strX = cformat(d=x, rank=0) canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont) x+= (xTop - xLow)/stepX - + y=yLow for i in range(stepY+1): yc=yTopOffset+plotHeight-(y-yLow)*yScale @@ -556,13 +556,13 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid strY = "%d" %y canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont) y+= (yTop - yLow)/stepY - + #draw label labelFont=pid.Font(ttf="tahoma",size=17,bold=0) if XLabel: canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0, yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor) - + if YLabel: canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0, font=labelFont,color=labelColor,angle=90) @@ -578,34 +578,34 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor plotHeight = canvas.size[1] - yTopOffset - yBottomOffset if plotHeight<=0 or plotWidth<=0: return - + NNN = len(data) if NNN < 2 or NNN != len(label): return if variance and len(variance)!=NNN: variance = [] - + Y2 = data[:] if variance: for i in range(NNN): if variance[i]: Y2 += [data[i]-variance[i]] - + #Y axis YLow, YTop, stepY = detScale(min(Y2), max(Y2)) YScale = plotHeight/(YTop - YLow) - + if YLow < 0 and YTop > 0: drawZero = 1 else: drawZero = 0 - + #X axis X = range(NNN) - Xll= 0 + Xll= 0 Xur= NNN-1 - - + + if drawZero: YZero = yTopOffset+plotHeight-YScale*(0-YLow) canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero) @@ -616,9 +616,9 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor if spaceWidth < 1: spaceWidth = 1 barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN) - + xc= xLeftOffset - scaleFont=pid.Font(ttf="verdana",size=11,bold=0) + scaleFont=pid.Font(ttf="verdana",size=11,bold=0) for i in range(NNN): yc = yTopOffset+plotHeight-(data[i]-YLow)*YScale canvas.drawRect(xc,YZero,xc+barWidth-1, yc, edgeColor=barColor,fillColor=barColor) @@ -633,13 +633,13 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor canvas.drawLine(xc+barWidth/2-2,yc+varlen,xc+barWidth/2+2,yc+varlen,color=pid.red) strX = label[i] canvas.drawString(strX,xc+barWidth/2.0+2,yTopOffset+plotHeight+2+canvas.stringWidth(strX,font=scaleFont),font=scaleFont,angle=90) - xc += barWidth + spaceWidth - + xc += barWidth + spaceWidth + #draw drawing region canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight) - + #draw Y scale - scaleFont=pid.Font(ttf="cour",size=16,bold=1) + scaleFont=pid.Font(ttf="cour",size=16,bold=1) y=YLow for i in range(stepY+1): yc=yTopOffset+plotHeight-(y-YLow)*YScale @@ -647,35 +647,35 @@ def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor strY = cformat(d=y, rank=0) canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont) y+= (YTop - YLow)/stepY - + #draw label labelFont=pid.Font(ttf="verdana",size=17,bold=0) if XLabel: canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,yTopOffset+plotHeight+65,font=labelFont,color=labelColor) - + if YLabel: canvas.drawString(YLabel,xLeftOffset-50, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,font=labelFont,color=labelColor,angle=90) - + labelFont=pid.Font(ttf="verdana",size=18,bold=0) if title: canvas.drawString(title,xLeftOffset,yTopOffset-15,font=labelFont,color=labelColor) - + return - + def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, axesColor=pid.black, labelColor=pid.black, lineSize="thin", lineColor=pid.grey, idFont="arial", idColor=pid.blue, idSize="14", symbolColor=pid.black, symbolType="circle", filled="yes", symbolSize="tiny", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1, bufferSpace = 15): 'displayR : correlation scatter plot, loadings : loading plot' - + dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX)) - + #get ID font size - idFontSize = int(idSize) - + idFontSize = int(idSize) + #If filled is yes, set fill color if filled == "yes": fillColor = symbolColor else: - fillColor = None - + fillColor = None + if symbolSize == "large": sizeModifier = 7 fontModifier = 12 @@ -687,8 +687,8 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax fontModifier = 3 else: sizeModifier = 1 - fontModifier = -1 - + fontModifier = -1 + if rank == 0: # Pearson correlation bufferSpace = 0 dataXPrimary = dataX @@ -700,7 +700,7 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax dataYPrimary = dataYRanked dataXAlt = dataX #Values used just for printing the other corr type to the graph image dataYAlt = dataY #Values used just for printing the other corr type to the graph image - + xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset plotHeight = canvas.size[1] - yTopOffset - yBottomOffset @@ -708,29 +708,29 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax return if len(dataXPrimary) < 1 or len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)): return - + max_X=max(dataXPrimary) min_X=min(dataXPrimary) max_Y=max(dataYPrimary) min_Y=min(dataYPrimary) - + #for some reason I forgot why I need to do this if loadingPlot: min_X = min(-0.1,min_X) max_X = max(0.1,max_X) min_Y = min(-0.1,min_Y) max_Y = max(0.1,max_Y) - + xLow, xTop, stepX=detScale(min_X,max_X) yLow, yTop, stepY=detScale(min_Y,max_Y) xScale = plotWidth/(xTop-xLow) yScale = plotHeight/(yTop-yLow) - + #draw drawing region canvas.drawRect(xLeftOffset-bufferSpace, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace) canvas.drawRect(xLeftOffset-bufferSpace+1, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace-1) - #calculate data points + #calculate data points data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary) xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary) @@ -767,12 +767,12 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax elif (symbolType == "diamond" and filled != "yes"): canvas.drawString(",", item[0]-canvas.stringWidth(",",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor) elif (symbolType == "diamond" and filled == "yes"): - canvas.drawString("D", item[0]-canvas.stringWidth("D",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor) + canvas.drawString("D", item[0]-canvas.stringWidth("D",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor) elif symbolType == "4-star": - canvas.drawString("l", item[0]-canvas.stringWidth("l",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor) + canvas.drawString("l", item[0]-canvas.stringWidth("l",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor) elif symbolType == "3-star": - canvas.drawString("k", item[0]-canvas.stringWidth("k",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor) - else: + canvas.drawString("k", item[0]-canvas.stringWidth("k",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor) + else: canvas.drawCross(item[0],item[1]-2,color=symbolColor, size=sizeModifier+2) if showLabel and dataLabel: @@ -784,10 +784,10 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax labelGap = 11 canvas.drawString(dataLabel[i], item[0]- canvas.stringWidth(dataLabel[i], font=labelFont)/2 + 1, item[1]+(labelGap+sizeModifier+(idFontSize-12)), font=labelFont, color=idColor) - + #draw scale scaleFont=pid.Font(ttf="cour",size=16,bold=1) - + x=xLow for i in range(stepX+1): @@ -795,14 +795,14 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax if ((x == 0) & (rank == 1)): pass else: - canvas.drawLine(xc,yTopOffset+plotHeight + bufferSpace,xc,yTopOffset+plotHeight+5 + bufferSpace, color=axesColor) + canvas.drawLine(xc,yTopOffset+plotHeight + bufferSpace,xc,yTopOffset+plotHeight+5 + bufferSpace, color=axesColor) strX = cformat(d=x, rank=rank) if ((strX == "0") & (rank == 1)): pass else: canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+20 + bufferSpace,font=scaleFont) x+= (xTop - xLow)/stepX - + y=yLow for i in range(stepY+1): yc=yTopOffset+plotHeight-(y-yLow)*yScale @@ -816,23 +816,23 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax else: canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)- 10 - bufferSpace,yc+4,font=scaleFont) y+= (yTop - yLow)/stepY - + #draw label labelFont=pid.Font(ttf="verdana",size=canvas.size[0]/45,bold=0) titleFont=pid.Font(ttf="verdana",size=canvas.size[0]/40,bold=0) - + if (rank == 1 and not title): canvas.drawString("Spearman Rank Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Spearman Rank Correlation",font=titleFont))/2.0, 25,font=titleFont,color=labelColor) elif (rank == 0 and not title): canvas.drawString("Pearson Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Pearson Correlation",font=titleFont))/2.0, 25,font=titleFont,color=labelColor) - + if XLabel: canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0, yTopOffset+plotHeight+yBottomOffset-25,font=labelFont,color=labelColor) - + if YLabel: canvas.drawString(YLabel, xLeftOffset-65, yTopOffset+plotHeight- (plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0, font=labelFont,color=labelColor,angle=90) @@ -841,7 +841,7 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax if title: canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0, 20,font=labelFont,color=labelColor) - + if fitcurve: import sys sys.argv = [ "mod_python" ] @@ -852,9 +852,9 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax AA = dot(fitXX,swapaxes(fitXX,0,1)) BB = dot(fitXX,fitYY) bb = la.linear_least_squares(AA,BB)[0] - + xc1 = xLeftOffset - yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale + yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale if yc1 > yTopOffset+plotHeight: yc1 = yTopOffset+plotHeight xc1 = (yLow-bb[0])/bb[1] @@ -865,8 +865,8 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax xc1=(xc1-xLow)*xScale+xLeftOffset else: pass - - xc2 = xLeftOffset + plotWidth + + xc2 = xLeftOffset + plotWidth yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale if yc2 > yTopOffset+plotHeight: yc2 = yTopOffset+plotHeight @@ -885,8 +885,8 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax if lineSize == "thick": canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor) canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace-1,xc2,yc2-1,color=lineColor) - - + + if displayR: labelFont=pid.Font(ttf="trebuc",size=canvas.size[0]/60,bold=0) NNN = len(dataX) @@ -901,7 +901,7 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax ZValue = 0.5*log((1.0+corr)/(1.0-corr)) ZValue = ZValue*sqrt(NNN-3) corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue))) - + NStr = "N = %d" % NNN strLenN = canvas.stringWidth(NStr,font=labelFont) @@ -924,24 +924,24 @@ def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, ax def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black", axesColor="black", labelColor="black", symbolColor="red", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1): 'displayR : correlation scatter plot, loadings : loading plot' - + dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX)) - - # Switching Ranked and Unranked X and Y values if a Spearman Rank Correlation + + # Switching Ranked and Unranked X and Y values if a Spearman Rank Correlation if rank == 0: dataXPrimary = dataX dataYPrimary = dataY dataXAlt = dataXRanked - dataYAlt = dataYRanked - - else: + dataYAlt = dataYRanked + + else: dataXPrimary = dataXRanked dataYPrimary = dataYRanked dataXAlt = dataX dataYAlt = dataY - + xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = drawSpace.attributes['width'] - xLeftOffset - xRightOffset plotHeight = drawSpace.attributes['height'] - yTopOffset - yBottomOffset @@ -949,34 +949,34 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" return if len(dataXPrimary) < 1 or len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)): return - + max_X=max(dataXPrimary) min_X=min(dataXPrimary) max_Y=max(dataYPrimary) min_Y=min(dataYPrimary) - + #for some reason I forgot why I need to do this if loadingPlot: min_X = min(-0.1,min_X) max_X = max(0.1,max_X) min_Y = min(-0.1,min_Y) max_Y = max(0.1,max_Y) - + xLow, xTop, stepX=detScale(min_X,max_X) yLow, yTop, stepY=detScale(min_Y,max_Y) xScale = plotWidth/(xTop-xLow) yScale = plotHeight/(yTop-yLow) - + #draw drawing region r = svg.rect(xLeftOffset, yTopOffset, plotWidth, plotHeight, 'none', axesColor, 1) drawSpace.addElement(r) - - #calculate data points + + #calculate data points data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary) xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary) labelFontF = "verdana" labelFontS = 11 - + if loadingPlot: xZero = -xLow*xScale+xLeftOffset yZero = yTopOffset+plotHeight+yLow*yScale @@ -988,7 +988,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" #drawSpace.drawPolygon(xCoord,edgeColor=plotColor,closed=0) else: pass - + for i, item in enumerate(xCoord): if dataLabel and dataLabel[i] in specialCases: drawSpace.addElement(svg.rect(item[0]-3, item[1]-3, 6, 6, "none", "green", 0.5)) @@ -998,11 +998,11 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" drawSpace.addElement(svg.line(item[0]+5,item[1],item[0]-5,item[1],symbolColor,1)) if showLabel and dataLabel: pass - drawSpace.addElement(svg.text(item[0], item[1]+14, dataLabel[i], labelFontS, + drawSpace.addElement(svg.text(item[0], item[1]+14, dataLabel[i], labelFontS, labelFontF, text_anchor="middle", style="stroke:blue;stroke-width:0.5;")) #canvas.drawString(, item[0]- canvas.stringWidth(dataLabel[i], # font=labelFont)/2, item[1]+14, font=labelFont, color=pid.blue) - + #draw scale #scaleFont=pid.Font(ttf="cour",size=14,bold=1) x=xLow @@ -1012,7 +1012,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" strX = cformat(d=x, rank=rank) drawSpace.addElement(svg.text(xc,yTopOffset+plotHeight+20,strX,13, "courier", text_anchor="middle")) x+= (xTop - xLow)/stepX - + y=yLow for i in range(stepY+1): yc=yTopOffset+plotHeight-(y-yLow)*yScale @@ -1020,7 +1020,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" strY = cformat(d=y, rank=rank) drawSpace.addElement(svg.text(xLeftOffset-10,yc+5,strY,13, "courier", text_anchor="end")) y+= (yTop - yLow)/stepY - + #draw label labelFontF = "verdana" labelFontS = 17 @@ -1028,7 +1028,7 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" drawSpace.addElement(svg.text(xLeftOffset+plotWidth/2.0, yTopOffset+plotHeight+yBottomOffset-10,XLabel, labelFontS, labelFontF, text_anchor="middle")) - + if YLabel: drawSpace.addElement(svg.text(xLeftOffset-50, yTopOffset+plotHeight/2,YLabel, @@ -1046,9 +1046,9 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" AA = dot(fitXX,swapaxes(fitXX,0,1)) BB = dot(fitXX,fitYY) bb = la.linear_least_squares(AA,BB)[0] - + xc1 = xLeftOffset - yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale + yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale if yc1 > yTopOffset+plotHeight: yc1 = yTopOffset+plotHeight xc1 = (yLow-bb[0])/bb[1] @@ -1059,8 +1059,8 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" xc1=(xc1-xLow)*xScale+xLeftOffset else: pass - - xc2 = xLeftOffset + plotWidth + + xc2 = xLeftOffset + plotWidth yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale if yc2 > yTopOffset+plotHeight: yc2 = yTopOffset+plotHeight @@ -1074,8 +1074,8 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" pass drawSpace.addElement(svg.line(xc1,yc1,xc2,yc2,"green", 1)) - - if displayR: + + if displayR: labelFontF = "trebuc" labelFontS = 14 NNN = len(dataX) @@ -1091,24 +1091,24 @@ def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black" ZValue = 0.5*log((1.0+corr)/(1.0-corr)) ZValue = ZValue*sqrt(NNN-3) corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue))) - + NStr = "N of Cases=%d" % NNN - + if rank == 1: corrStr = "Spearman's r=%1.3f P=%3.2E" % (corr, corrPValue) else: corrStr = "Pearson's r=%1.3f P=%3.2E" % (corr, corrPValue) - + drawSpace.addElement(svg.text(xLeftOffset,yTopOffset-10,NStr, labelFontS, labelFontF, text_anchor="start")) drawSpace.addElement(svg.text(xLeftOffset+plotWidth,yTopOffset-25,corrStr, labelFontS, labelFontF, text_anchor="end")) - """ + """ """ return -# This function determines the scale of the plot +# This function determines the scale of the plot def detScaleOld(min,max): if min>=max: return None @@ -1205,8 +1205,8 @@ def colorSpectrumOld(n): colors.append(pid.Color(red,green,blue)) i += 1 return colors - - + + def bluefunc(x): @@ -1273,7 +1273,7 @@ def BWSpectrum(n=100): return [pid.Color(0,0,0),pid.Color(1,1,1)] elif n == 3: return [pid.Color(0,0,0),pid.Color(0.5,0.5,0.5),pid.Color(1,1,1)] - + step = 1.0/n x = 0.0 out = [] diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py index 82511228..03f8b9b3 100644 --- a/wqflask/wqflask/show_trait/show_trait_page.py +++ b/wqflask/wqflask/show_trait/show_trait_page.py @@ -42,9 +42,9 @@ class ShowTraitPage(DataEditingPage): if not self.openMysql(): return - + TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') - + if traitInfos: database,ProbeSetID,CellID = traitInfos else: @@ -61,7 +61,7 @@ class ShowTraitPage(DataEditingPage): if thisTrait.db.type == "ProbeSet": - self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers + self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM ProbeSetFreeze WHERE Name = "%s"''' % database) indId, indName, indFullName, confidential, AuthorisedUsers = self.cursor.fetchall()[0] @@ -86,7 +86,7 @@ class ShowTraitPage(DataEditingPage): at this time, please go back and select other database." % indFullName] self.error(heading=heading,detail=detail,error="Confidential Database") return - + user_ip = fd.remote_ip query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \ UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400" @@ -105,26 +105,26 @@ class ShowTraitPage(DataEditingPage): pass else: pass - + if thisTrait.db.type != 'ProbeSet' and thisTrait.cellid: heading = "Retrieve Data" detail = ['The Record you requested doesn\'t exist!'] self.error(heading=heading,detail=detail) return - #XZ: Aug 23, 2010: I commented out this block because this feature is not used anymore + #XZ: Aug 23, 2010: I commented out this block because this feature is not used anymore # check if animal information are available """ self.cursor.execute(''' - SELECT - SampleXRef.ProbeFreezeId - FROM - SampleXRef, ProbeSetFreeze - WHERE + SELECT + SampleXRef.ProbeFreezeId + FROM + SampleXRef, ProbeSetFreeze + WHERE SampleXRef.ProbeFreezeId = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = "%s" - ''' % thisTrait.db.name) - + ''' % thisTrait.db.name) + sampleId = self.cursor.fetchall() if sampleId: thisTrait.strainInfo = 1 @@ -136,12 +136,12 @@ class ShowTraitPage(DataEditingPage): fd.identification = '%s : %s'%(thisTrait.db.shortname,ProbeSetID) thisTrait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\ &ProbeSetID=%s&RISet=%s&parentsf1=on' %(database,ProbeSetID,fd.RISet) - + if CellID: fd.identification = '%s/%s'%(fd.identification, CellID) thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL, CellID) - - #retrieve trait information + + #retrieve trait information try: thisTrait.retrieveInfo() thisTrait.retrieveData() @@ -153,18 +153,16 @@ class ShowTraitPage(DataEditingPage): detail = ["The information you requested is not avaiable at this time."] self.error(heading=heading,detail=detail) return - + ##read genotype file fd.RISet = thisTrait.riset fd.readGenotype() - + if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())): fd.displayVariance = 1 fd.varianceDispName = 'SE' fd.formID = 'varianceChoice' - + self.dict['body']= thisTrait DataEditingPage.__init__(self, fd, thisTrait) self.dict['title'] = '%s: Display Trait' % fd.identification - - diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 3e1c2729..611cc05b 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -5,6 +5,7 @@ from wqflask import app from flask import render_template, request from wqflask import search_results +from wqflask.show_trait import show_trait_page from pprint import pformat as pf @@ -20,4 +21,5 @@ def search(): @app.route("/showDatabaseBXD") def showDatabaseBXD(): + template_vars = show_trait_page.ShowTraitPage(request.args) return render_template("trait_data_and_analysis.html") -- cgit 1.4.1 From 8ac39ead1014953c634e85d0ce340497ecfe2934 Mon Sep 17 00:00:00 2001 From: Sam Ockman Date: Tue, 5 Jun 2012 00:24:44 -0400 Subject: Ran reindent.py recursively on wqflask directory --- .gitignore | 2 + wqflask/base/GeneralObject.py | 77 +- wqflask/base/admin.py | 32 +- wqflask/base/cgiData.py | 60 +- wqflask/base/cookieData.py | 27 +- wqflask/base/header.py | 2 +- wqflask/base/indexBody.py | 414 +-- wqflask/base/myCookie.py | 38 +- wqflask/base/sessionData.py | 27 +- wqflask/base/template.py | 74 +- wqflask/base/templatePage.py | 318 +- wqflask/base/webqtlCaseData.py | 43 +- wqflask/base/webqtlDataset.py | 249 +- wqflask/base/webqtlFormData.py | 516 +-- wqflask/base/webqtlTrait.py | 1152 +++--- .../basicStatistics/BasicStatisticsFunctions.py | 280 +- .../basicStatistics/BasicStatisticsPage_alpha.py | 602 ++-- .../basicStatistics/updatedBasicStatisticsPage.py | 284 +- wqflask/dbFunction/webqtlDatabaseFunction.py | 293 +- wqflask/utility/AJAX_table.py | 224 +- wqflask/utility/Plot.py | 2304 ++++++------ wqflask/utility/TDCell.py | 15 +- wqflask/utility/THCell.py | 16 +- wqflask/utility/svg.py | 133 +- wqflask/utility/webqtlUtil.py | 1459 ++++---- wqflask/wqflask/show_trait/DataEditingPage.py | 3810 ++++++++++---------- wqflask/wqflask/show_trait/show_trait_page.py | 290 +- 27 files changed, 6353 insertions(+), 6388 deletions(-) (limited to 'wqflask/utility') diff --git a/.gitignore b/.gitignore index 8bc78454..fc051245 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,6 @@ # gitignore *.pyc *.orig +*.bak *~ + diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py index 311c9e22..53d1357b 100755 --- a/wqflask/base/GeneralObject.py +++ b/wqflask/base/GeneralObject.py @@ -25,47 +25,44 @@ # Last updated by GeneNetwork Core Team 2010/10/20 class GeneralObject: - """ - Base class to define an Object. - a = [Spam(1, 4), Spam(9, 3), Spam(4,6)] - a.sort(lambda x, y: cmp(x.eggs, y.eggs)) - """ + """ + Base class to define an Object. + a = [Spam(1, 4), Spam(9, 3), Spam(4,6)] + a.sort(lambda x, y: cmp(x.eggs, y.eggs)) + """ - def __init__(self, *args, **kw): - self.contents = list(args) - for name, value in kw.items(): - setattr(self, name, value) - - def __setitem__(self, key, value): - setattr(self, key, value) - - def __getitem__(self, key): - return getattr(self, key) - - def __getattr__(self, key): - if key in self.__dict__.keys(): - return self.__dict__[key] - else: - return eval("self.__dict__.%s" % key) - - def __len__(self): - return len(self.__dict__) - 1 - - def __str__(self): - s = '' - for key in self.__dict__.keys(): - if key != 'contents': - s += '%s = %s\n' % (key,self.__dict__[key]) - return s - - def __repr__(self): - s = '' - for key in self.__dict__.keys(): - s += '%s = %s\n' % (key,self.__dict__[key]) - return s - - def __cmp__(self,other): - return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys())) + def __init__(self, *args, **kw): + self.contents = list(args) + for name, value in kw.items(): + setattr(self, name, value) + def __setitem__(self, key, value): + setattr(self, key, value) + def __getitem__(self, key): + return getattr(self, key) + def __getattr__(self, key): + if key in self.__dict__.keys(): + return self.__dict__[key] + else: + return eval("self.__dict__.%s" % key) + + def __len__(self): + return len(self.__dict__) - 1 + + def __str__(self): + s = '' + for key in self.__dict__.keys(): + if key != 'contents': + s += '%s = %s\n' % (key,self.__dict__[key]) + return s + + def __repr__(self): + s = '' + for key in self.__dict__.keys(): + s += '%s = %s\n' % (key,self.__dict__[key]) + return s + + def __cmp__(self,other): + return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys())) diff --git a/wqflask/base/admin.py b/wqflask/base/admin.py index a04df2da..1ba75117 100755 --- a/wqflask/base/admin.py +++ b/wqflask/base/admin.py @@ -35,18 +35,18 @@ ADMIN_search_dbs = { - 'rat': {'PERITONEAL FAT': ['FT_2A_0605_Rz'], + 'rat': {'PERITONEAL FAT': ['FT_2A_0605_Rz'], 'KIDNEY': ['KI_2A_0405_Rz'], 'ADRENAL GLAND': ['HXB_Adrenal_1208'], 'HEART': ['HXB_Heart_1208'] }, - 'mouse': {'CEREBELLUM': ['CB_M_0305_R'], + 'mouse': {'CEREBELLUM': ['CB_M_0305_R'], 'STRIATUM': ['SA_M2_0905_R', 'SA_M2_0405_RC', 'UTHSC_1107_RankInv', 'Striatum_Exon_0209'], - 'HIPPOCAMPUS': ['HC_M2_0606_R', 'UMUTAffyExon_0209_RMA'], - 'WHOLE BRAIN': ['BR_M2_1106_R', 'IBR_M_0106_R', 'BRF2_M_0805_R', 'UCLA_BHF2_BRAIN_0605'], - 'LIVER': ['LV_G_0106_B', 'UCLA_BHF2_LIVER_0605'], - 'EYE': ['Eye_M2_0908_R'], - 'HEMATOPOIETIC STEM CELLS': ['HC_U_0304_R'], + 'HIPPOCAMPUS': ['HC_M2_0606_R', 'UMUTAffyExon_0209_RMA'], + 'WHOLE BRAIN': ['BR_M2_1106_R', 'IBR_M_0106_R', 'BRF2_M_0805_R', 'UCLA_BHF2_BRAIN_0605'], + 'LIVER': ['LV_G_0106_B', 'UCLA_BHF2_LIVER_0605'], + 'EYE': ['Eye_M2_0908_R'], + 'HEMATOPOIETIC STEM CELLS': ['HC_U_0304_R'], 'KIDNEY': ['MA_M2_0806_R'], 'MAMMARY TUMORS': ['MA_M_0704_R', 'NCI_Agil_Mam_Tum_RMA_0409'], 'PREFRONTAL CORTEX': ['VCUSal_1206_R'], @@ -65,14 +65,14 @@ ADMIN_search_dbs = { ###LIST of tissue alias -ADMIN_tissue_alias = {'CEREBELLUM': ['Cb'], - 'STRIATUM': ['Str'], - 'HIPPOCAMPUS': ['Hip'], - 'WHOLE BRAIN': ['Brn'], - 'LIVER': ['Liv'], - 'EYE': ['Eye'], - 'PERITONEAL FAT': ['Fat'], - 'HEMATOPOIETIC STEM CELLS': ['Hsc'], +ADMIN_tissue_alias = {'CEREBELLUM': ['Cb'], + 'STRIATUM': ['Str'], + 'HIPPOCAMPUS': ['Hip'], + 'WHOLE BRAIN': ['Brn'], + 'LIVER': ['Liv'], + 'EYE': ['Eye'], + 'PERITONEAL FAT': ['Fat'], + 'HEMATOPOIETIC STEM CELLS': ['Hsc'], 'KIDNEY': ['Kid'], 'ADRENAL GLAND': ['Adr'], 'HEART': ['Hea'], @@ -84,5 +84,3 @@ ADMIN_tissue_alias = {'CEREBELLUM': ['Cb'], 'ADIPOSE': ['Wfat'], 'RETINA': ['Ret'] } - - diff --git a/wqflask/base/cgiData.py b/wqflask/base/cgiData.py index 57416060..155b3ec3 100755 --- a/wqflask/base/cgiData.py +++ b/wqflask/base/cgiData.py @@ -30,41 +30,37 @@ ######################################### class cgiData(dict): - '''convert Field storage object to Dict object - Filed storage object cannot be properly dumped - ''' + '''convert Field storage object to Dict object + Filed storage object cannot be properly dumped + ''' - def __init__(self, field_storage=None): + def __init__(self, field_storage=None): - if not field_storage: - field_storage={} - - for key in field_storage.keys(): - temp = field_storage.getlist(key) - if len(temp) > 1: - temp = map(self.toValue, temp) - elif len(temp) == 1: - temp = self.toValue(temp[0]) - else: - temp = None - self[key]= temp - - def toValue(self, obj): - '''fieldstorge returns different type of objects, \ - need to convert to string or None''' - try: - return obj.value - except: - return "" - - def getvalue(self, k, default= None): - try: - return self[k] - except: - return default - - getfirst = getvalue + if not field_storage: + field_storage={} + for key in field_storage.keys(): + temp = field_storage.getlist(key) + if len(temp) > 1: + temp = map(self.toValue, temp) + elif len(temp) == 1: + temp = self.toValue(temp[0]) + else: + temp = None + self[key]= temp + def toValue(self, obj): + '''fieldstorge returns different type of objects, \ + need to convert to string or None''' + try: + return obj.value + except: + return "" + def getvalue(self, k, default= None): + try: + return self[k] + except: + return default + getfirst = getvalue diff --git a/wqflask/base/cookieData.py b/wqflask/base/cookieData.py index 4b7c9046..eeb7c0cf 100755 --- a/wqflask/base/cookieData.py +++ b/wqflask/base/cookieData.py @@ -30,23 +30,20 @@ ######################################### class cookieData(dict): - 'convert mod python Cookie object to Dict object' + 'convert mod python Cookie object to Dict object' - def __init__(self, cookies=None): + def __init__(self, cookies=None): - if not cookies: - cookies={} - - for key in cookies.keys(): - self[key.lower()]= cookies[key].value - - def getvalue(self, k, default= None): - try: - return self[k.lower()] - except: - return default - - getfirst = getvalue + if not cookies: + cookies={} + for key in cookies.keys(): + self[key.lower()]= cookies[key].value + def getvalue(self, k, default= None): + try: + return self[k.lower()] + except: + return default + getfirst = getvalue diff --git a/wqflask/base/header.py b/wqflask/base/header.py index b6136b51..ec15e174 100755 --- a/wqflask/base/header.py +++ b/wqflask/base/header.py @@ -3,4 +3,4 @@ import webqtlConfig header_string = open(webqtlConfig.HTMLPATH + 'header.html', 'r').read() header_string = header_string.replace("\\'", "'") header_string = header_string.replace('%"','%%"') -header_string = header_string.replace('', '%s') \ No newline at end of file +header_string = header_string.replace('', '%s') diff --git a/wqflask/base/indexBody.py b/wqflask/base/indexBody.py index aa67dffa..a5bc4c17 100755 --- a/wqflask/base/indexBody.py +++ b/wqflask/base/indexBody.py @@ -1,174 +1,174 @@ index_body_string = """ -

Select and Search -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +

Select and Search + + +

- Species: - - - -
- Group: - - - -
- Type: - - - -
- Database: - - - - -
- - -

    Databases marked with ** suffix are not public yet. -
    Access requires user login.

-
- Get Any: - - - - -
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + - + - + + - - + + - + - - + + - - - - + + + - -
+ Species: + + + +
+ Group: + + + +
+ Type: + + + +
+ Database: + + + + +
+ + +

    Databases marked with ** suffix are not public yet. +
    Access requires user login.

+
+ Get Any: + + + + +
- +
+ - -

    Enter terms, genes, ID numbers in the Get Any field. -
    Use * or ? wildcards (Cyp*a?, synap*). -
    Use Combined for terms such as tyrosine kinase.

+ 		+

    Enter terms, genes, ID numbers in the Get Any field. +
    Use * or ? wildcards (Cyp*a?, synap*). +
    Use Combined for terms such as tyrosine kinase.

-
- Combined: -
+ Combined: + - + - - -
+ + +
- - -      -      - +
+ + +      +      + -
- - - -
- + + + + + + + + @@ -185,7 +185,7 @@ Quick HELP Examples and User's Guide

-  You can also use advanced commands. Copy these simple examples +  You can also use advanced commands. Copy these simple examples
  into the Get Any or Combined search fields:
    @@ -206,85 +206,85 @@ Quick HELP Examples and
  • RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)
    in Combined finds diabetes-associated transcripts with peak trans eQTLs on Chr 2 between 100 and 105 Mb with LRS scores between 9 and 999. -
+ - + -

Websites Affiliated with GeneNetwork

-

-

-

-

____________________________ - -

Getting Started   

-
    -
  1. Select Species (or select All) -
  2. Select Group (a specific sample) -
  3. Select Type of data: -
      -
    • Phenotype (traits) -
    • Genotype (markers) -
    • Expression (mRNAs) -
    -
  4. Select a Database -
  5. Enter search terms in the Get Any or Combined field: words, genes, ID numbers, probes, advanced search commands -
  6. Click on the Search button -
  7. Optional: Use the Make Default button to save your preferences -
- -

____________________________ +

Websites Affiliated with GeneNetwork

+

+

+

+

____________________________ + +

Getting Started   

+
    +
  1. Select Species (or select All) +
  2. Select Group (a specific sample) +
  3. Select Type of data: +
      +
    • Phenotype (traits) +
    • Genotype (markers) +
    • Expression (mRNAs) +
    +
  4. Select a Database +
  5. Enter search terms in the Get Any or Combined field: words, genes, ID numbers, probes, advanced search commands +
  6. Click on the Search button +
  7. Optional: Use the Make Default button to save your preferences +
+ +

____________________________

How to Use GeneNetwork -

-

Take a 20-40 minute GeneNetwork Tour that includes screen shots and typical steps in the analysis.

-
-
-

For information about resources and methods, select the INFO buttons.

+
+

Take a 20-40 minute GeneNetwork Tour that includes screen shots and typical steps in the analysis.

+
+
+

For information about resources and methods, select the INFO buttons.

+ + - -

Try the Workstation site to explore data and features that are being implemented.

-

Review the Conditions and Contacts pages for information on the status of data sets and advice on their use and citation.

+

Review the Conditions and Contacts pages for information on the status of data sets and advice on their use and citation.

+ +
-
- -

Mirror and Development Sites

+

Mirror and Development Sites

- + -

History and Archive +

History and Archive -

-

GeneNetwork's Time Machine links to earlier versions that correspond to specific publication dates.

+
+

GeneNetwork's Time Machine links to earlier versions that correspond to specific publication dates.

-
+

- + """ diff --git a/wqflask/base/myCookie.py b/wqflask/base/myCookie.py index db5320df..add7e6ea 100755 --- a/wqflask/base/myCookie.py +++ b/wqflask/base/myCookie.py @@ -25,31 +25,27 @@ # Last updated by GeneNetwork Core Team 2010/10/20 ######################################### -## python cookie and mod python cookie are +## python cookie and mod python cookie are ## not compatible ######################################### class myCookie(dict): - 'define my own cookie' - - def __init__(self, name="", value="", expire = None, path="/"): - self['name']= name - self['value']= value - self['expire']= expire - self['path']= path - - def __getattr__(self, key): - if key in self.keys(): - return self[key] - else: - return None - - def __nonzero__ (self): - if self['name']: - return 1 - else: - return 0 - + 'define my own cookie' + def __init__(self, name="", value="", expire = None, path="/"): + self['name']= name + self['value']= value + self['expire']= expire + self['path']= path + def __getattr__(self, key): + if key in self.keys(): + return self[key] + else: + return None + def __nonzero__ (self): + if self['name']: + return 1 + else: + return 0 diff --git a/wqflask/base/sessionData.py b/wqflask/base/sessionData.py index 01555f87..4b23060f 100755 --- a/wqflask/base/sessionData.py +++ b/wqflask/base/sessionData.py @@ -30,24 +30,21 @@ ######################################### class sessionData(dict): - 'convert mod python Session object to Dict object' + 'convert mod python Session object to Dict object' - def __init__(self, mod_python_session=None): - - if not mod_python_session: - mod_python_session = {} + def __init__(self, mod_python_session=None): - for key in mod_python_session.keys(): - self[key]= mod_python_session[key] - - - def getvalue(self, k, default= None): - try: - return self[k] - except: - return default + if not mod_python_session: + mod_python_session = {} - getfirst = getvalue + for key in mod_python_session.keys(): + self[key]= mod_python_session[key] + def getvalue(self, k, default= None): + try: + return self[k] + except: + return default + getfirst = getvalue diff --git a/wqflask/base/template.py b/wqflask/base/template.py index 85bd86df..aa8f90dc 100755 --- a/wqflask/base/template.py +++ b/wqflask/base/template.py @@ -68,32 +68,32 @@ template = """ %s - - - - %s - - + + + + %s + + - - - - - + + + + + - - - - + + + +
- - - %s - -
-
+ + + %s + +
+
- %s
-
+ %s
+
@@ -103,20 +103,20 @@ template = """ diff --git a/wqflask/base/templatePage.py b/wqflask/base/templatePage.py index 821c6181..7ef58a72 100755 --- a/wqflask/base/templatePage.py +++ b/wqflask/base/templatePage.py @@ -61,162 +61,162 @@ from utility import webqtlUtil class templatePage: - contents = ['title','basehref','js1','js2', 'layer', 'header', 'body', 'footer'] - - # you can pass in another template here if you want - def __init__(self, fd=None, template=template.template): - - # initiate dictionary - self.starttime = time.time() - self.dict = {} - self.template = template - - for item in self.contents: - self.dict[item] = "" - - self.dict['basehref'] = "" #webqtlConfig.BASEHREF - self.cursor = None - - self.cookie = [] #XZ: list to hold cookies (myCookie object) being changed - self.content_type = 'text/html' - self.content_disposition = '' - self.redirection = '' - self.debug = '' - self.attachment = '' - - #XZ: Holding data (new data or existing data being changed) that should be saved to session. The data must be picklable!!! - self.session_data_changed = {} - - self.userName = 'Guest' - self.privilege = 'guest' - - # Commenting this out for flask - we'll have to reimplement later - Sam - #if fd.input_session_data.has_key('user'): - # self.userName = fd.input_session_data['user'] - #if fd.input_session_data.has_key('privilege'): - # self.privilege = fd.input_session_data['privilege'] - - def __str__(self): - - #XZ: default setting - thisUserName = self.userName - thisPrivilege = self.privilege - #XZ: user may just go through login or logoff page - if self.session_data_changed.has_key('user'): - thisUserName = self.session_data_changed['user'] - if self.session_data_changed.has_key('privilege'): - thisPrivilege = self.session_data_changed['privilege'] - - if thisUserName == 'Guest': - userInfo = 'Welcome! Login' - else: - userInfo = 'Hi, %s! Logout' % thisUserName - - reload(header) - self.dict['header'] = header.header_string % userInfo - - serverInfo = "It took %2.3f second(s) for %s to generate this page" % (time.time()-self.starttime, socket.getfqdn()) - reload(footer) - self.dict['footer'] = footer.footer_string % serverInfo - - slist = [] - for item in self.contents: - slist.append(self.dict[item]) - return self.template % tuple(slist) - - - def __del__(self): - if self.cursor: - self.cursor.close() - - def write(self): - 'return string representation of this object' - - if self.cursor: - self.cursor.close() - - return str(self) - - def writeFile(self, filename): - 'save string representation of this object into a file' - if self.cursor: - self.cursor.close() - - try: - 'it could take a long time to generate the file, save to .tmp first' - fp = open(os.path.join(webqtlConfig.TMPDIR, filename+'.tmp'), 'wb') - fp.write(str(self)) - fp.close() - path_tmp = os.path.join(webqtlConfig.TMPDIR, filename+'.tmp') - path_html = os.path.join(webqtlConfig.TMPDIR, filename) - shutil.move(path_tmp,path_html) - except: - pass - - def openMysql(self): - try: - self.con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, \ - user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) - self.cursor = self.con.cursor() - return 1 - except: - heading = "Connect MySQL Server" - detail = ["Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_SERVER+"':100061. \ - The server may be down at this time"] - self.error(heading=heading,detail=detail,error="Error 2003") - return 0 - - def updMysql(self): - try: - self.con = MySQLdb.Connect(db=webqtlConfig.DB_UPDNAME,host=webqtlConfig.MYSQL_UPDSERVER, \ - user=webqtlConfig.DB_UPDUSER,passwd=webqtlConfig.DB_UPDPASSWD) - self.cursor = self.con.cursor() - return 1 - except: - heading = "Connect MySQL Server" - detail = ["update: Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_UPDSERVER+"':100061. \ - The server may be down at this time "] - self.error(heading=heading,detail=detail,error="Error 2003") - return 0 - - def error(self,heading="",intro=[],detail=[],title="Error",error="Error"): - 'generating a WebQTL style error page' - Heading = HT.Paragraph(heading) - Heading.__setattr__("class","title") - - Intro = HT.Blockquote() - if intro: - for item in intro: - Intro.append(item) - else: - Intro.append(HT.Strong('Sorry!'),' Error occurred while processing\ - your request.', HT.P(),'The nature of the error generated is as\ - follows:') - - Detail = HT.Blockquote() - Detail.append(HT.Span("%s : " % error,Class="fwb cr")) - if detail: - Detail2 = HT.Blockquote() - for item in detail: - Detail2.append(item) - Detail.append(HT.Italic(Detail2)) - - #Detail.__setattr__("class","subtitle") - TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="top") - TD_LR.append(Heading,Intro,Detail) - self.dict['body'] = str(TD_LR) - self.dict['title'] = title - - def session(self,mytitle="",myHeading=""): - 'generate a auto-refreshing temporary html file(waiting page)' - self.filename = webqtlUtil.generate_session() - self.dict['title'] = mytitle - self.dict['basehref'] = webqtlConfig.REFRESHSTR % (webqtlConfig.CGIDIR, self.filename) + "" #webqtlConfig.BASEHREF - - TD_LR = HT.TD(align="center", valign="middle", height=200,width="100%", bgColor='#eeeeee') - Heading = HT.Paragraph(myHeading, Class="fwb fs16 cr") - # NL, 07/27/2010. variable 'PROGRESSBAR' has been moved from templatePage.py to webqtlUtil.py; - TD_LR.append(Heading, HT.BR(), webqtlUtil.PROGRESSBAR) - self.dict['body'] = TD_LR - self.writeFile(self.filename + '.html') - return self.filename + contents = ['title','basehref','js1','js2', 'layer', 'header', 'body', 'footer'] + + # you can pass in another template here if you want + def __init__(self, fd=None, template=template.template): + + # initiate dictionary + self.starttime = time.time() + self.dict = {} + self.template = template + + for item in self.contents: + self.dict[item] = "" + + self.dict['basehref'] = "" #webqtlConfig.BASEHREF + self.cursor = None + + self.cookie = [] #XZ: list to hold cookies (myCookie object) being changed + self.content_type = 'text/html' + self.content_disposition = '' + self.redirection = '' + self.debug = '' + self.attachment = '' + + #XZ: Holding data (new data or existing data being changed) that should be saved to session. The data must be picklable!!! + self.session_data_changed = {} + + self.userName = 'Guest' + self.privilege = 'guest' + + # Commenting this out for flask - we'll have to reimplement later - Sam + #if fd.input_session_data.has_key('user'): + # self.userName = fd.input_session_data['user'] + #if fd.input_session_data.has_key('privilege'): + # self.privilege = fd.input_session_data['privilege'] + + def __str__(self): + + #XZ: default setting + thisUserName = self.userName + thisPrivilege = self.privilege + #XZ: user may just go through login or logoff page + if self.session_data_changed.has_key('user'): + thisUserName = self.session_data_changed['user'] + if self.session_data_changed.has_key('privilege'): + thisPrivilege = self.session_data_changed['privilege'] + + if thisUserName == 'Guest': + userInfo = 'Welcome! Login' + else: + userInfo = 'Hi, %s! Logout' % thisUserName + + reload(header) + self.dict['header'] = header.header_string % userInfo + + serverInfo = "It took %2.3f second(s) for %s to generate this page" % (time.time()-self.starttime, socket.getfqdn()) + reload(footer) + self.dict['footer'] = footer.footer_string % serverInfo + + slist = [] + for item in self.contents: + slist.append(self.dict[item]) + return self.template % tuple(slist) + + + def __del__(self): + if self.cursor: + self.cursor.close() + + def write(self): + 'return string representation of this object' + + if self.cursor: + self.cursor.close() + + return str(self) + + def writeFile(self, filename): + 'save string representation of this object into a file' + if self.cursor: + self.cursor.close() + + try: + 'it could take a long time to generate the file, save to .tmp first' + fp = open(os.path.join(webqtlConfig.TMPDIR, filename+'.tmp'), 'wb') + fp.write(str(self)) + fp.close() + path_tmp = os.path.join(webqtlConfig.TMPDIR, filename+'.tmp') + path_html = os.path.join(webqtlConfig.TMPDIR, filename) + shutil.move(path_tmp,path_html) + except: + pass + + def openMysql(self): + try: + self.con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, \ + user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) + self.cursor = self.con.cursor() + return 1 + except: + heading = "Connect MySQL Server" + detail = ["Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_SERVER+"':100061. \ + The server may be down at this time"] + self.error(heading=heading,detail=detail,error="Error 2003") + return 0 + + def updMysql(self): + try: + self.con = MySQLdb.Connect(db=webqtlConfig.DB_UPDNAME,host=webqtlConfig.MYSQL_UPDSERVER, \ + user=webqtlConfig.DB_UPDUSER,passwd=webqtlConfig.DB_UPDPASSWD) + self.cursor = self.con.cursor() + return 1 + except: + heading = "Connect MySQL Server" + detail = ["update: Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_UPDSERVER+"':100061. \ + The server may be down at this time "] + self.error(heading=heading,detail=detail,error="Error 2003") + return 0 + + def error(self,heading="",intro=[],detail=[],title="Error",error="Error"): + 'generating a WebQTL style error page' + Heading = HT.Paragraph(heading) + Heading.__setattr__("class","title") + + Intro = HT.Blockquote() + if intro: + for item in intro: + Intro.append(item) + else: + Intro.append(HT.Strong('Sorry!'),' Error occurred while processing\ + your request.', HT.P(),'The nature of the error generated is as\ + follows:') + + Detail = HT.Blockquote() + Detail.append(HT.Span("%s : " % error,Class="fwb cr")) + if detail: + Detail2 = HT.Blockquote() + for item in detail: + Detail2.append(item) + Detail.append(HT.Italic(Detail2)) + + #Detail.__setattr__("class","subtitle") + TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="top") + TD_LR.append(Heading,Intro,Detail) + self.dict['body'] = str(TD_LR) + self.dict['title'] = title + + def session(self,mytitle="",myHeading=""): + 'generate a auto-refreshing temporary html file(waiting page)' + self.filename = webqtlUtil.generate_session() + self.dict['title'] = mytitle + self.dict['basehref'] = webqtlConfig.REFRESHSTR % (webqtlConfig.CGIDIR, self.filename) + "" #webqtlConfig.BASEHREF + + TD_LR = HT.TD(align="center", valign="middle", height=200,width="100%", bgColor='#eeeeee') + Heading = HT.Paragraph(myHeading, Class="fwb fs16 cr") + # NL, 07/27/2010. variable 'PROGRESSBAR' has been moved from templatePage.py to webqtlUtil.py; + TD_LR.append(Heading, HT.BR(), webqtlUtil.PROGRESSBAR) + self.dict['body'] = TD_LR + self.writeFile(self.filename + '.html') + return self.filename diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 4df32ca4..f68354be 100755 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -25,30 +25,27 @@ # Last updated by GeneNetwork Core Team 2010/10/20 class webqtlCaseData: - """ - one case data in one trait - """ + """ + one case data in one trait + """ - val = None #Trait Value - var = None #Trait Variance - N = None #Number of individuals - - def __init__(self, val=val, var=var, N=N): - self.val = val - self.var = var - self.N = N - - def __str__(self): - str = "" - if self.val != None: - str += "value=%2.3f" % self.val - if self.var != None: - str += " variance=%2.3f" % self.var - if self.N != None: - str += " ndata=%d" % self.N - return str - - __repr__ = __str__ + val = None #Trait Value + var = None #Trait Variance + N = None #Number of individuals + def __init__(self, val=val, var=var, N=N): + self.val = val + self.var = var + self.N = N + def __str__(self): + str = "" + if self.val != None: + str += "value=%2.3f" % self.val + if self.var != None: + str += " variance=%2.3f" % self.var + if self.N != None: + str += " ndata=%d" % self.N + return str + __repr__ = __str__ diff --git a/wqflask/base/webqtlDataset.py b/wqflask/base/webqtlDataset.py index da1b8601..f8491bb1 100755 --- a/wqflask/base/webqtlDataset.py +++ b/wqflask/base/webqtlDataset.py @@ -31,130 +31,125 @@ import webqtlConfig class webqtlDataset: - """ - Database class defines a database in webqtl, can be either Microarray, - Published phenotype, genotype, or user input database(temp) - """ - - def __init__(self, dbName, cursor=None): - - assert dbName - self.id = 0 - self.name = '' - self.type = '' - self.riset = '' - self.cursor = cursor - - #temporary storage - if dbName.find('Temp') >= 0: - self.searchfield = ['name','description'] - self.disfield = ['name','description'] - self.type = 'Temp' - self.id = 1 - self.fullname = 'Temporary Storage' - self.shortname = 'Temp' - elif dbName.find('Publish') >= 0: - self.searchfield = ['name','post_publication_description','abstract','title','authors'] - self.disfield = ['name','pubmed_id', - 'pre_publication_description', 'post_publication_description', 'original_description', - 'pre_publication_abbreviation', 'post_publication_abbreviation', - 'lab_code', 'submitter', 'owner', 'authorized_users', - 'authors','title','abstract', 'journal','volume','pages','month', - 'year','sequence', 'units', 'comments'] - self.type = 'Publish' - elif dbName.find('Geno') >= 0: - self.searchfield = ['name','chr'] - self.disfield = ['name','chr','mb', 'source2', 'sequence'] - self.type = 'Geno' - else: #ProbeSet - self.searchfield = ['name','description','probe_target_description', - 'symbol','alias','genbankid','unigeneid','omim', - 'refseq_transcriptid','probe_set_specificity', 'probe_set_blat_score'] - self.disfield = ['name','symbol','description','probe_target_description', - 'chr','mb','alias','geneid','genbankid', 'unigeneid', 'omim', - 'refseq_transcriptid','blatseq','targetseq','chipid', 'comments', - 'strand_probe','strand_gene','probe_set_target_region', - 'probe_set_specificity', 'probe_set_blat_score','probe_set_blat_mb_start', - 'probe_set_blat_mb_end', 'probe_set_strand', - 'probe_set_note_by_rw', 'flag'] - self.type = 'ProbeSet' - self.name = dbName - if self.cursor and self.id == 0: - self.retrieveName() - - def __str__(self): - return self.name - - __repr__ = __str__ - - - def getRISet(self): - assert self.cursor - if self.type == 'Publish': - query = ''' - SELECT - InbredSet.Name, InbredSet.Id - FROM - InbredSet, PublishFreeze - WHERE - PublishFreeze.InbredSetId = InbredSet.Id AND - PublishFreeze.Name = "%s" - ''' % self.name - elif self.type == 'Geno': - query = ''' - SELECT - InbredSet.Name, InbredSet.Id - FROM - InbredSet, GenoFreeze - WHERE - GenoFreeze.InbredSetId = InbredSet.Id AND - GenoFreeze.Name = "%s" - ''' % self.name - elif self.type == 'ProbeSet': - query = ''' - SELECT - InbredSet.Name, InbredSet.Id - FROM - InbredSet, ProbeSetFreeze, ProbeFreeze - WHERE - ProbeFreeze.InbredSetId = InbredSet.Id AND - ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND - ProbeSetFreeze.Name = "%s" - ''' % self.name - else: - return "" - self.cursor.execute(query) - RISet, RIID = self.cursor.fetchone() - if RISet == 'BXD300': - RISet = "BXD" - self.riset = RISet - self.risetid = RIID - return RISet - - - def retrieveName(self): - assert self.id == 0 and self.cursor - query = ''' - SELECT - Id, Name, FullName, ShortName - FROM - %sFreeze - WHERE - public > %d AND - (Name = "%s" OR FullName = "%s" OR ShortName = "%s") - '''% (self.type, webqtlConfig.PUBLICTHRESH, self.name, self.name, self.name) - try: - self.cursor.execute(query) - self.id,self.name,self.fullname,self.shortname=self.cursor.fetchone() - except: - raise KeyError, `self.name`+' doesn\'t exist.' - - - def genHTML(self, Class='c0dd'): - return HT.Href(text = HT.Span('%s Database' % self.fullname, Class= "fwb " + Class), - url= webqtlConfig.INFOPAGEHREF % self.name,target="_blank") - - - - - + """ + Database class defines a database in webqtl, can be either Microarray, + Published phenotype, genotype, or user input database(temp) + """ + + def __init__(self, dbName, cursor=None): + + assert dbName + self.id = 0 + self.name = '' + self.type = '' + self.riset = '' + self.cursor = cursor + + #temporary storage + if dbName.find('Temp') >= 0: + self.searchfield = ['name','description'] + self.disfield = ['name','description'] + self.type = 'Temp' + self.id = 1 + self.fullname = 'Temporary Storage' + self.shortname = 'Temp' + elif dbName.find('Publish') >= 0: + self.searchfield = ['name','post_publication_description','abstract','title','authors'] + self.disfield = ['name','pubmed_id', + 'pre_publication_description', 'post_publication_description', 'original_description', + 'pre_publication_abbreviation', 'post_publication_abbreviation', + 'lab_code', 'submitter', 'owner', 'authorized_users', + 'authors','title','abstract', 'journal','volume','pages','month', + 'year','sequence', 'units', 'comments'] + self.type = 'Publish' + elif dbName.find('Geno') >= 0: + self.searchfield = ['name','chr'] + self.disfield = ['name','chr','mb', 'source2', 'sequence'] + self.type = 'Geno' + else: #ProbeSet + self.searchfield = ['name','description','probe_target_description', + 'symbol','alias','genbankid','unigeneid','omim', + 'refseq_transcriptid','probe_set_specificity', 'probe_set_blat_score'] + self.disfield = ['name','symbol','description','probe_target_description', + 'chr','mb','alias','geneid','genbankid', 'unigeneid', 'omim', + 'refseq_transcriptid','blatseq','targetseq','chipid', 'comments', + 'strand_probe','strand_gene','probe_set_target_region', + 'probe_set_specificity', 'probe_set_blat_score','probe_set_blat_mb_start', + 'probe_set_blat_mb_end', 'probe_set_strand', + 'probe_set_note_by_rw', 'flag'] + self.type = 'ProbeSet' + self.name = dbName + if self.cursor and self.id == 0: + self.retrieveName() + + def __str__(self): + return self.name + + __repr__ = __str__ + + + def getRISet(self): + assert self.cursor + if self.type == 'Publish': + query = ''' + SELECT + InbredSet.Name, InbredSet.Id + FROM + InbredSet, PublishFreeze + WHERE + PublishFreeze.InbredSetId = InbredSet.Id AND + PublishFreeze.Name = "%s" + ''' % self.name + elif self.type == 'Geno': + query = ''' + SELECT + InbredSet.Name, InbredSet.Id + FROM + InbredSet, GenoFreeze + WHERE + GenoFreeze.InbredSetId = InbredSet.Id AND + GenoFreeze.Name = "%s" + ''' % self.name + elif self.type == 'ProbeSet': + query = ''' + SELECT + InbredSet.Name, InbredSet.Id + FROM + InbredSet, ProbeSetFreeze, ProbeFreeze + WHERE + ProbeFreeze.InbredSetId = InbredSet.Id AND + ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND + ProbeSetFreeze.Name = "%s" + ''' % self.name + else: + return "" + self.cursor.execute(query) + RISet, RIID = self.cursor.fetchone() + if RISet == 'BXD300': + RISet = "BXD" + self.riset = RISet + self.risetid = RIID + return RISet + + + def retrieveName(self): + assert self.id == 0 and self.cursor + query = ''' + SELECT + Id, Name, FullName, ShortName + FROM + %sFreeze + WHERE + public > %d AND + (Name = "%s" OR FullName = "%s" OR ShortName = "%s") + '''% (self.type, webqtlConfig.PUBLICTHRESH, self.name, self.name, self.name) + try: + self.cursor.execute(query) + self.id,self.name,self.fullname,self.shortname=self.cursor.fetchone() + except: + raise KeyError, `self.name`+' doesn\'t exist.' + + + def genHTML(self, Class='c0dd'): + return HT.Href(text = HT.Span('%s Database' % self.fullname, Class= "fwb " + Class), + url= webqtlConfig.INFOPAGEHREF % self.name,target="_blank") diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index c94dbe53..06faacc0 100755 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py @@ -40,261 +40,261 @@ from utility import webqtlUtil class webqtlFormData: - 'Represents data from a WebQTL form page, needed to generate the next page' - attrs = ('formID','RISet','genotype','strainlist','allstrainlist', - 'suggestive','significance','submitID','identification', 'enablevariance', - 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') - - #XZ: Attention! All attribute values must be picklable! - - def __init__(self, start_vars = None, req = None, mod_python_session=None, FieldStorage_formdata=None): - - self.__dict__.update(start_vars) - - for item in self.attrs: - setattr(self,item, None) - - try: - self.remote_ip = req.connection.remote_ip - except: - self.remote_ip = '1.2.3.4' - - if req and req.headers_in.has_key('referer'): - self.refURL = req.headers_in['referer'] - else: - self.refURL = None - - # For now let's just comment all this out - Sam - - #self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie. - # - ##XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable. - #self.input_session_data = sessionData.sessionData( mod_python_session ) - # - ##XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data. - #self.formdata = cgiData( FieldStorage_formdata ) - # - ##get Form ID - #self.formID = self.formdata.getfirst('FormID') - # - ##get rest of the attributes - #if self.formID: - # for item in self.attrs: - # value = self.formdata.getfirst(item) - # if value != None: - # setattr(self,item,string.strip(value)) - - self.ppolar = "" - self.mpolar = "" - if self.RISet: - try: - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - f1, f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.RISet] - except: - f1 = f12 = self.mpolar = self.ppolar = None - - try: - self.nperm = int(self.nperm) - self.nboot = int(self.nboot) - except: - self.nperm = 2000 #XZ: Rob asked to change the default value to 2000 - self.nboot = 2000 #XZ: Rob asked to change the default value to 2000 - - if self.allstrainlist: - self.allstrainlist = map(string.strip, string.split(self.allstrainlist)) - #self.readGenotype() - #self.readData() - - if self.RISet == 'BXD300': - self.RISet = 'BXD' - else: - pass - - def __getitem__(self, key): - return self.__dict__[key] - - def get(self, key, default=None): - if key in self.__dict__: - return self.__dict__[key] - else: - return default - - def __str__(self): - rstr = '' - for item in self.attrs: - if item != 'genotype': - rstr += '%s:%s\n' % (item,str(getattr(self,item))) - return rstr - - - def readGenotype(self): - 'read genotype from .geno file' - if self.RISet == 'BXD300': - self.RISet = 'BXD' - else: - pass - assert self.RISet - #genotype_1 is Dataset Object without parents and f1 - #genotype_2 is Dataset Object with parents and f1 (not for intercross) - self.genotype_1 = reaper.Dataset() - self.genotype_1.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno')) - try: - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet] - except: - _f1 = _f12 = _mat = _pat = None - - self.genotype_2 =self.genotype_1 - if self.genotype_1.type == "riset" and _mat and _pat: - self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1) - - #determine default genotype object - if self.incparentsf1 and self.genotype_1.type != "intercross": - self.genotype = self.genotype_2 - else: - self.incparentsf1 = 0 - self.genotype = self.genotype_1 - self.strainlist = list(self.genotype.prgy) - self.f1list = self.parlist = [] - if _f1 and _f12: - self.f1list = [_f1, _f12] - if _mat and _pat: - self.parlist = [_mat, _pat] - - def readData(self, strainlst=[], incf1=[]): - 'read user input data or from trait data and analysis form' - - if not self.genotype: - self.readGenotype() - if not strainlst: - if incf1: - strainlst = self.f1list + self.strainlist - else: - strainlst = self.strainlist - - - traitfiledata = self.formdata.getfirst('traitfile') - traitpastedata = self.formdata.getfirst('traitpaste') - variancefiledata = self.formdata.getfirst('variancefile') - variancepastedata = self.formdata.getfirst('variancepaste') - Nfiledata = self.formdata.getfirst('Nfile') - - - if traitfiledata: - tt = string.split(traitfiledata) - vals = map(webqtlUtil.StringAsFloat, tt) - elif traitpastedata: - tt = string.split(traitpastedata) - vals = map(webqtlUtil.StringAsFloat, tt) - else: - vals = map(self.FormDataAsFloat, strainlst) - - if len(vals) < len(strainlst): - vals += [None]*(len(strainlst) - len(vals)) - elif len(vals) > len(strainlst): - vals = vals[:len(strainlst)] - else: - pass - - - if variancefiledata: - tt = string.split(variancefiledata) - vars = map(webqtlUtil.StringAsFloat, tt) - elif variancepastedata: - tt = string.split(variancepastedata) - vars = map(webqtlUtil.StringAsFloat, tt) - else: - vars = map(self.FormVarianceAsFloat, strainlst) - - if len(vars) < len(strainlst): - vars += [None]*(len(strainlst) - len(vars)) - elif len(vars) > len(strainlst): - vars = vars[:len(strainlst)] - else: - pass - - if Nfiledata: - tt = string.split(Nfiledata) - nstrains = map(webqtlUtil.IntAsFloat, tt) - if len(nstrains) < len(strainlst): - nstrains += [None]*(len(strainlst) - len(nstrains)) - else: - nstrains = map(self.FormNAsFloat, strainlst) - - ##vals, vars, nstrains is obsolete - self.allTraitData = {} - for i, _strain in enumerate(strainlst): - if vals[i] != None: - self.allTraitData[_strain] = webqtlCaseData(vals[i], vars[i], nstrains[i]) - - - - def informativeStrains(self, strainlst=[], incVars = 0): - '''if readData was called, use this to output the informative strains - (strain with values)''' - if not strainlst: - strainlst = self.strainlist - strains = [] - vals = [] - vars = [] - for _strain in strainlst: - if self.allTraitData.has_key(_strain): - _val, _var = self.allTraitData[_strain].val, self.allTraitData[_strain].var - if _val != None: - if incVars: - if _var != None: - strains.append(_strain) - vals.append(_val) - vars.append(_var) - else: - strains.append(_strain) - vals.append(_val) - vars.append(None) - return strains, vals, vars, len(strains) - - - - def FormDataAsFloat(self, key): - try: - return float(self.formdata.getfirst(key)) - except: - return None - - - def FormVarianceAsFloat(self, key): - try: - return float(self.formdata.getfirst('V' + key)) - except: - return None - - def FormNAsFloat(self, key): - try: - return int(self.formdata.getfirst('N' + key)) - except: - return None - - def Sample(self): - 'Create some dummy data for testing' - self.RISet = 'BXD' - self.incparentsf1 = 'on' - #self.display = 9.2 - #self.significance = 16.1 - self.readGenotype() - self.identification = 'BXD : Coat color example by Lu Lu, et al' - #self.readGenotype() - #self.genotype.ReadMM('AXBXAforQTL') - #self.strainlist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy) - #self.strainlist.sort() - self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2), - 'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2), - 'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4), - 'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2), - 'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3), - 'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3), - 'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2), - 'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4), - 'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4), - 'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1), - 'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4), - 'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4), - 'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)} + 'Represents data from a WebQTL form page, needed to generate the next page' + attrs = ('formID','RISet','genotype','strainlist','allstrainlist', + 'suggestive','significance','submitID','identification', 'enablevariance', + 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') + + #XZ: Attention! All attribute values must be picklable! + + def __init__(self, start_vars = None, req = None, mod_python_session=None, FieldStorage_formdata=None): + + self.__dict__.update(start_vars) + + for item in self.attrs: + setattr(self,item, None) + + try: + self.remote_ip = req.connection.remote_ip + except: + self.remote_ip = '1.2.3.4' + + if req and req.headers_in.has_key('referer'): + self.refURL = req.headers_in['referer'] + else: + self.refURL = None + + # For now let's just comment all this out - Sam + + #self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie. + # + ##XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable. + #self.input_session_data = sessionData.sessionData( mod_python_session ) + # + ##XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data. + #self.formdata = cgiData( FieldStorage_formdata ) + # + ##get Form ID + #self.formID = self.formdata.getfirst('FormID') + # + ##get rest of the attributes + #if self.formID: + # for item in self.attrs: + # value = self.formdata.getfirst(item) + # if value != None: + # setattr(self,item,string.strip(value)) + + self.ppolar = "" + self.mpolar = "" + if self.RISet: + try: + # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; + f1, f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.RISet] + except: + f1 = f12 = self.mpolar = self.ppolar = None + + try: + self.nperm = int(self.nperm) + self.nboot = int(self.nboot) + except: + self.nperm = 2000 #XZ: Rob asked to change the default value to 2000 + self.nboot = 2000 #XZ: Rob asked to change the default value to 2000 + + if self.allstrainlist: + self.allstrainlist = map(string.strip, string.split(self.allstrainlist)) + #self.readGenotype() + #self.readData() + + if self.RISet == 'BXD300': + self.RISet = 'BXD' + else: + pass + + def __getitem__(self, key): + return self.__dict__[key] + + def get(self, key, default=None): + if key in self.__dict__: + return self.__dict__[key] + else: + return default + + def __str__(self): + rstr = '' + for item in self.attrs: + if item != 'genotype': + rstr += '%s:%s\n' % (item,str(getattr(self,item))) + return rstr + + + def readGenotype(self): + 'read genotype from .geno file' + if self.RISet == 'BXD300': + self.RISet = 'BXD' + else: + pass + assert self.RISet + #genotype_1 is Dataset Object without parents and f1 + #genotype_2 is Dataset Object with parents and f1 (not for intercross) + self.genotype_1 = reaper.Dataset() + self.genotype_1.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno')) + try: + # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; + _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet] + except: + _f1 = _f12 = _mat = _pat = None + + self.genotype_2 =self.genotype_1 + if self.genotype_1.type == "riset" and _mat and _pat: + self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1) + + #determine default genotype object + if self.incparentsf1 and self.genotype_1.type != "intercross": + self.genotype = self.genotype_2 + else: + self.incparentsf1 = 0 + self.genotype = self.genotype_1 + self.strainlist = list(self.genotype.prgy) + self.f1list = self.parlist = [] + if _f1 and _f12: + self.f1list = [_f1, _f12] + if _mat and _pat: + self.parlist = [_mat, _pat] + + def readData(self, strainlst=[], incf1=[]): + 'read user input data or from trait data and analysis form' + + if not self.genotype: + self.readGenotype() + if not strainlst: + if incf1: + strainlst = self.f1list + self.strainlist + else: + strainlst = self.strainlist + + + traitfiledata = self.formdata.getfirst('traitfile') + traitpastedata = self.formdata.getfirst('traitpaste') + variancefiledata = self.formdata.getfirst('variancefile') + variancepastedata = self.formdata.getfirst('variancepaste') + Nfiledata = self.formdata.getfirst('Nfile') + + + if traitfiledata: + tt = string.split(traitfiledata) + vals = map(webqtlUtil.StringAsFloat, tt) + elif traitpastedata: + tt = string.split(traitpastedata) + vals = map(webqtlUtil.StringAsFloat, tt) + else: + vals = map(self.FormDataAsFloat, strainlst) + + if len(vals) < len(strainlst): + vals += [None]*(len(strainlst) - len(vals)) + elif len(vals) > len(strainlst): + vals = vals[:len(strainlst)] + else: + pass + + + if variancefiledata: + tt = string.split(variancefiledata) + vars = map(webqtlUtil.StringAsFloat, tt) + elif variancepastedata: + tt = string.split(variancepastedata) + vars = map(webqtlUtil.StringAsFloat, tt) + else: + vars = map(self.FormVarianceAsFloat, strainlst) + + if len(vars) < len(strainlst): + vars += [None]*(len(strainlst) - len(vars)) + elif len(vars) > len(strainlst): + vars = vars[:len(strainlst)] + else: + pass + + if Nfiledata: + tt = string.split(Nfiledata) + nstrains = map(webqtlUtil.IntAsFloat, tt) + if len(nstrains) < len(strainlst): + nstrains += [None]*(len(strainlst) - len(nstrains)) + else: + nstrains = map(self.FormNAsFloat, strainlst) + + ##vals, vars, nstrains is obsolete + self.allTraitData = {} + for i, _strain in enumerate(strainlst): + if vals[i] != None: + self.allTraitData[_strain] = webqtlCaseData(vals[i], vars[i], nstrains[i]) + + + + def informativeStrains(self, strainlst=[], incVars = 0): + '''if readData was called, use this to output the informative strains + (strain with values)''' + if not strainlst: + strainlst = self.strainlist + strains = [] + vals = [] + vars = [] + for _strain in strainlst: + if self.allTraitData.has_key(_strain): + _val, _var = self.allTraitData[_strain].val, self.allTraitData[_strain].var + if _val != None: + if incVars: + if _var != None: + strains.append(_strain) + vals.append(_val) + vars.append(_var) + else: + strains.append(_strain) + vals.append(_val) + vars.append(None) + return strains, vals, vars, len(strains) + + + + def FormDataAsFloat(self, key): + try: + return float(self.formdata.getfirst(key)) + except: + return None + + + def FormVarianceAsFloat(self, key): + try: + return float(self.formdata.getfirst('V' + key)) + except: + return None + + def FormNAsFloat(self, key): + try: + return int(self.formdata.getfirst('N' + key)) + except: + return None + + def Sample(self): + 'Create some dummy data for testing' + self.RISet = 'BXD' + self.incparentsf1 = 'on' + #self.display = 9.2 + #self.significance = 16.1 + self.readGenotype() + self.identification = 'BXD : Coat color example by Lu Lu, et al' + #self.readGenotype() + #self.genotype.ReadMM('AXBXAforQTL') + #self.strainlist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy) + #self.strainlist.sort() + self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2), + 'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2), + 'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4), + 'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2), + 'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3), + 'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3), + 'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2), + 'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4), + 'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4), + 'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1), + 'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4), + 'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4), + 'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)} diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py index 88226894..812d112a 100755 --- a/wqflask/base/webqtlTrait.py +++ b/wqflask/base/webqtlTrait.py @@ -14,579 +14,579 @@ from pprint import pformat as pf class webqtlTrait: - """ - Trait class defines a trait in webqtl, can be either Microarray, - Published phenotype, genotype, or user input trait - - """ - - def __init__(self, cursor = None, **kw): - print("in webqtlTrait") - self.cursor = cursor - self.db = None # database object - self.name = '' # Trait ID, ProbeSet ID, Published ID, etc. - self.cellid = '' - self.identification = 'un-named trait' - self.riset = '' - self.haveinfo = 0 - self.sequence = '' # Blat sequence, available for ProbeSet - self.data = {} - print("foo") - print("kw in webqtlTrait are:", pf(kw)) - print("printed\n\n") - for name, value in kw.items(): - if self.__dict__.has_key(name): - setattr(self, name, value) - elif name == 'fullname': - name2 = value.split("::") - if len(name2) == 2: - self.db, self.name = name2 - elif len(name2) == 3: - self.db, self.name, self.cellid = name2 - else: - raise KeyError, repr(value) + ' parameter format error.' - else: - raise KeyError, repr(name) + ' not a valid parameter for this class.' - - if self.db and isinstance(self.db, basestring): - assert self.cursor, "Don't have a cursor" - self.db = webqtlDataset(self.db, self.cursor) - - #if self.db == None, not from a database - print("self.db is:", self.db, type(self.db)) - if self.db: - if self.db.type == "Temp": - self.cursor.execute(''' - SELECT - InbredSet.Name - FROM - InbredSet, Temp - WHERE - Temp.InbredSetId = InbredSet.Id AND - Temp.Name = "%s" - ''', self.name) - self.riset = self.cursor.fetchone()[0] - else: - self.riset = self.db.getRISet() - - # - # In ProbeSet, there are maybe several annotations match one sequence - # so we need use sequence(BlatSeq) as the identification, when we update - # one annotation, we update the others who match the sequence also. - # - # Hongqiang Li, 3/3/2008 - # - - #XZ, 05/08/2009: This block is not neccessary. We can add 'BlatSeq' into disfield. - # The variable self.sequence should be changed to self.BlatSeq - # It also should be changed in other places where it are used. - - if self.db: - if self.db.type == 'ProbeSet': - print("Doing ProbeSet Query") - query = ''' - SELECT - ProbeSet.BlatSeq - FROM - ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSet.Id=ProbeSetXRef.ProbeSetId and - ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and - ProbeSet.Name = %s and - ProbeSetFreeze.Name = %s - ''', (self.name, self.db.name) - print("query is:", query) - self.cursor.execute(*query) - self.sequence = self.cursor.fetchone()[0] - print("self.sequence is:", self.sequence) - - - def getName(self): - str = "" - if self.db and self.name: - str = "%s::%s" % (self.db, self.name) - if self.cellid: - str += "::" + self.cellid - else: - str = self.description - return str - - # - # when user enter a trait or GN generate a trait, user want show the name - # not the name that generated by GN randomly, the two follow function are - # used to give the real name and the database. displayName() will show the - # database also, getGivenName() just show the name. - # For other trait, displayName() as same as getName(), getGivenName() as - # same as self.name - # - # Hongqiang 11/29/07 - # - def getGivenName(self): - str = self.name - if self.db and self.name: - if self.db.type=='Temp': - self.cursor.execute('SELECT description FROM Temp WHERE Name=%s', self.name) - desc = self.cursor.fetchone()[0] - if desc.__contains__('PCA'): - desc = desc[desc.rindex(':')+1:].strip() - else: - desc = desc[:desc.index('entered')].strip() - str = desc - return str - - def displayName(self): - str = "" - if self.db and self.name: - if self.db.type=='Temp': - desc = self.description - if desc.__contains__('PCA'): - desc = desc[desc.rindex(':')+1:].strip() - else: - desc = desc[:desc.index('entered')].strip() - str = "%s::%s" % (self.db, desc) - else: - str = "%s::%s" % (self.db, self.name) - if self.cellid: - str += "::" + self.cellid - else: - str = self.description - - return str - - - #def __str__(self): - # #return "%s %s" % (self.getName(), self.riset) - # return self.getName() - __str__ = getName - __repr__ = __str__ - - def exportData(self, strainlist, type="val"): - """ - export data according to strainlist - mostly used in calculating correlation - """ - result = [] - for strain in strainlist: - if self.data.has_key(strain): - if type=='val': - result.append(self.data[strain].val) - elif type=='var': - result.append(self.data[strain].var) - elif type=='N': - result.append(self.data[strain].N) - else: - raise KeyError, `type`+' type is incorrect.' - else: - result.append(None) - return result - - def exportInformative(self, incVar=0): - """ - export informative strain - mostly used in qtl regression - """ - strains = [] - vals = [] - vars = [] - for strain, value in self.data.items(): - if value.val != None: - if not incVar or value.var != None: - strains.append(strain) - vals.append(value.val) - vars.append(value.var) - return strains, vals, vars - - - # - # In ProbeSet, there are maybe several annotations match one sequence - # so we need use sequence(BlatSeq) as the identification, when we update - # one annotation, we update the others who match the sequence also. - # - # Hongqiang Li, 3/3/2008 - # - def getSequence(self): - assert self.cursor - if self.db.type == 'ProbeSet': - self.cursor.execute(''' - SELECT - ProbeSet.BlatSeq - FROM - ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSet.Id=ProbeSetXRef.ProbeSetId and - ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and - ProbeSet.Name = %s - ProbeSetFreeze.Name = %s - ''', self.name, self.db.name) - #self.cursor.execute(query) - results = self.fetchone() - - return results[0] - - - - def retrieveData(self, strainlist=[]): - assert self.db and self.cursor - - if self.db.type == 'Temp': - query = ''' - SELECT - Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id - FROM - TempData, Temp, Strain - WHERE - TempData.StrainId = Strain.Id AND - TempData.Id = Temp.DataId AND - Temp.name = '%s' - Order BY - Strain.Name - ''' % self.name - #XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE - elif self.db.type == 'Publish': - query = ''' - SELECT - Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id - FROM - (PublishData, Strain, PublishXRef, PublishFreeze) - left join PublishSE on - (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId) - left join NStrain on - (NStrain.DataId = PublishData.Id AND - NStrain.StrainId = PublishData.StrainId) - WHERE - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND - PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id - Order BY - Strain.Name - ''' % (self.name, self.db.id) - - #XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE - elif self.cellid: - #Probe Data - query = ''' - SELECT - Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id - FROM - (ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, - Strain, Probe, ProbeSet) - left join ProbeSE on - (ProbeSE.DataId = ProbeData.Id AND ProbeSE.StrainId = ProbeData.StrainId) - WHERE - Probe.Name = '%s' AND ProbeSet.Name = '%s' AND - Probe.ProbeSetId = ProbeSet.Id AND - ProbeXRef.ProbeId = Probe.Id AND - ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND - ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeXRef.DataId = ProbeData.Id AND - ProbeData.StrainId = Strain.Id - Order BY - Strain.Name - ''' % (self.cellid, self.name, self.db.name) - #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE - elif self.db.type == 'ProbeSet': - #ProbeSet Data - query = ''' - SELECT - Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id - FROM - (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef) - left join ProbeSetSE on - (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) - WHERE - ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSetXRef.DataId = ProbeSetData.Id AND - ProbeSetData.StrainId = Strain.Id - Order BY - Strain.Name - ''' % (self.name, self.db.name) - #XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE - else: - #Geno Data - #XZ: The SpeciesId is not necessary, but it's nice to keep it to speed up database search. - query = ''' - SELECT - Strain.Name, GenoData.value, GenoSE.error, GenoData.Id - FROM - (GenoData, GenoFreeze, Strain, Geno, GenoXRef) - left join GenoSE on - (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) - WHERE - Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND - GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoFreeze.Name = '%s' AND - GenoXRef.DataId = GenoData.Id AND - GenoData.StrainId = Strain.Id - Order BY - Strain.Name - ''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.db.riset), self.name, self.db.name) - - - self.cursor.execute(query) - results = self.cursor.fetchall() - self.data.clear() - if results: - self.mysqlid = results[0][-1] - if strainlist: - for item in results: - if item[0] in strainlist: - val = item[1] - if val != None: - var = item[2] - ndata = None - if self.db.type in ('Publish', 'Temp'): - ndata = item[3] - self.data[item[0]] = webqtlCaseData(val, var, ndata) - #end for - else: - for item in results: - val = item[1] - if val != None: - var = item[2] - ndata = None - if self.db.type in ('Publish', 'Temp'): - ndata = item[3] - self.data[item[0]] = webqtlCaseData(val, var, ndata) - #end for - #end if - else: - pass - - def keys(self): - return self.__dict__.keys() - - def has_key(self, key): - return self.__dict__.has_key(key) - - def items(self): - return self.__dict__.items() - - def retrieveInfo(self, QTL = None): - assert self.db and self.cursor - if self.db.type == 'Publish': - #self.db.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\ - # 'Abstract', 'Journal','Volume','Pages','Month','Year','Sequence',\ - # 'Units', 'comments'] - query = ''' - SELECT - PublishXRef.Id, Publication.PubMed_ID, - Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, - Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, - Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, - Publication.Authors, Publication.Title, Publication.Abstract, - Publication.Journal, Publication.Volume, Publication.Pages, - Publication.Month, Publication.Year, PublishXRef.Sequence, - Phenotype.Units, PublishXRef.comments - FROM - PublishXRef, Publication, Phenotype, PublishFreeze - WHERE - PublishXRef.Id = %s AND - Phenotype.Id = PublishXRef.PhenotypeId AND - Publication.Id = PublishXRef.PublicationId AND - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishFreeze.Id =%s - ''' % (self.name, self.db.id) - #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name - #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. - elif self.db.type == 'ProbeSet': - disfieldString = string.join(self.db.disfield,',ProbeSet.') - disfieldString = 'ProbeSet.' + disfieldString - query = """ - SELECT %s - FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSet.Name = '%s' - """ % (disfieldString, self.db.name, self.name) - #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name - # to avoid the problem of same marker name from different species. - elif self.db.type == 'Geno': - disfieldString = string.join(self.db.disfield,',Geno.') - disfieldString = 'Geno.' + disfieldString - query = """ - SELECT %s - FROM Geno, GenoFreeze, GenoXRef - WHERE - GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoXRef.GenoId = Geno.Id AND - GenoFreeze.Name = '%s' AND - Geno.Name = '%s' - """ % (disfieldString, self.db.name, self.name) - else: #Temp type - query = 'SELECT %s FROM %s WHERE Name = "%s"' % \ - (string.join(self.db.disfield,','), self.db.type, self.name) - - - self.cursor.execute(query) - traitInfo = self.cursor.fetchone() - if traitInfo: - self.haveinfo = 1 - - #XZ: assign SQL query result to trait attributes. - for i, field in enumerate(self.db.disfield): - setattr(self, field, traitInfo[i]) - - if self.db.type == 'Publish': - self.confidential = 0 - if self.pre_publication_description and not self.pubmed_id: - self.confidential = 1 - - self.homologeneid = None - if self.db.type == 'ProbeSet' and self.riset and self.geneid: - #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number. - #XZ: So I have to test if geneid is number before execute the query. - #XZ: The geneid values in database should be cleaned up. - try: - junk = float(self.geneid) - geneidIsNumber = 1 - except: - geneidIsNumber = 0 - - if geneidIsNumber: - query = """ - SELECT - HomologeneId - FROM - Homologene, Species, InbredSet - WHERE - Homologene.GeneId =%s AND - InbredSet.Name = '%s' AND - InbredSet.SpeciesId = Species.Id AND - Species.TaxonomyId = Homologene.TaxonomyId - """ % (self.geneid, self.riset) - self.cursor.execute(query) - result = self.cursor.fetchone() - else: - result = None - - if result: - self.homologeneid = result[0] - - if QTL: - if self.db.type == 'ProbeSet' and not self.cellid: - query = ''' - SELECT - ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean - FROM - ProbeSetXRef, ProbeSet - WHERE - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSet.Name = "%s" AND - ProbeSetXRef.ProbeSetFreezeId =%s - ''' % (self.name, self.db.id) - self.cursor.execute(query) - traitQTL = self.cursor.fetchone() - if traitQTL: - self.locus, self.lrs, self.pvalue, self.mean = traitQTL - else: - self.locus = self.lrs = self.pvalue = self.mean = "" - if self.db.type == 'Publish': - query = ''' - SELECT - PublishXRef.Locus, PublishXRef.LRS - FROM - PublishXRef, PublishFreeze - WHERE - PublishXRef.Id = %s AND - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishFreeze.Id =%s - ''' % (self.name, self.db.id) - self.cursor.execute(query) - traitQTL = self.cursor.fetchone() - if traitQTL: - self.locus, self.lrs = traitQTL - else: - self.locus = self.lrs = "" - else: - raise KeyError, `self.name`+' information is not found in the database.' - - def genHTML(self, formName = "", dispFromDatabase=0, privilege="guest", userName="Guest", authorized_users=""): - if not self.haveinfo: - self.retrieveInfo() - - if self.db.type == 'Publish': - PubMedLink = "" - if self.pubmed_id: - PubMedLink = HT.Href(text="PubMed %d : " % self.pubmed_id, - target = "_blank", url = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id) - else: - PubMedLink = HT.Span("Unpublished : ", Class="fs15") - - if formName: - setDescription2 = HT.Href(url="javascript:showDatabase3('%s','%s','%s','')" % - (formName, self.db.name, self.name), Class = "fs14") - else: - setDescription2 = HT.Href(url="javascript:showDatabase2('%s','%s','')" % - (self.db.name,self.name), Class = "fs14") - - if self.confidential and not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=privilege, userName=userName, authorized_users=authorized_users): - setDescription2.append('RecordID/%s - %s' % (self.name, self.pre_publication_description)) - else: - setDescription2.append('RecordID/%s - %s' % (self.name, self.post_publication_description)) - - #XZ 03/26/2011: Xiaodong comment out the following two lins as Rob asked. Need to check with Rob why in PublishXRef table, there are few row whose Sequence > 1. - #if self.sequence > 1: - # setDescription2.append(' btach %d' % self.sequence) - if self.authors: - a1 = string.split(self.authors,',')[0] - while a1[0] == '"' or a1[0] == "'" : - a1 = a1[1:] - setDescription2.append(' by ') - setDescription2.append(HT.Italic('%s, and colleagues' % a1)) - setDescription = HT.Span(PubMedLink, setDescription2) - - elif self.db.type == 'Temp': - setDescription = HT.Href(text="%s" % (self.description),url="javascript:showDatabase2\ - ('%s','%s','')" % (self.db.name,self.name), Class = "fs14") - setDescription = HT.Span(setDescription) - - elif self.db.type == 'Geno': # Genome DB only available for single search - if formName: - setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\ - '%2.3f' % self.mb),url="javascript:showDatabase3('%s','%s','%s','')" % \ - (formName, self.db.name, self.name), Class = "fs14") - else: - setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\ - '%2.3f' % self.mb),url="javascript:showDatabase2('%s','%s','')" % \ - (self.db.name,self.name), Class = "fs14") - - setDescription = HT.Span(setDescription) - - else: - if self.cellid: - if formName: - setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name, self.cellid),url=\ - "javascript:showDatabase3('%s','%s','%s','%s')" % (formName, self.db.name,self.name,self.cellid), \ - Class = "fs14") - else: - setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name,self.cellid),url=\ - "javascript:showDatabase2('%s','%s','%s')" % (self.db.name,self.name,self.cellid), \ - Class = "fs14") - else: - if formName: - setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\ - "javascript:showDatabase3('%s','%s','%s','')" % (formName, self.db.name,self.name), \ - Class = "fs14") - else: - setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\ - "javascript:showDatabase2('%s','%s','')" % (self.db.name,self.name), \ - Class = "fs14") - if self.symbol and self.chr and self.mb: - setDescription.append(' [') - setDescription.append(HT.Italic('%s' % self.symbol,Class="cdg fwb")) - setDescription.append(' on Chr %s @ %s Mb]' % (self.chr,self.mb)) - if self.description: - setDescription.append(': %s' % self.description) - if self.probe_target_description: - setDescription.append('; %s' % self.probe_target_description) - setDescription = HT.Span(setDescription) - - if self.db.type != 'Temp' and dispFromDatabase: - setDescription.append( ' --- FROM : ') - setDescription.append(self.db.genHTML(Class='cori')) - return setDescription + """ + Trait class defines a trait in webqtl, can be either Microarray, + Published phenotype, genotype, or user input trait + + """ + + def __init__(self, cursor = None, **kw): + print("in webqtlTrait") + self.cursor = cursor + self.db = None # database object + self.name = '' # Trait ID, ProbeSet ID, Published ID, etc. + self.cellid = '' + self.identification = 'un-named trait' + self.riset = '' + self.haveinfo = 0 + self.sequence = '' # Blat sequence, available for ProbeSet + self.data = {} + print("foo") + print("kw in webqtlTrait are:", pf(kw)) + print("printed\n\n") + for name, value in kw.items(): + if self.__dict__.has_key(name): + setattr(self, name, value) + elif name == 'fullname': + name2 = value.split("::") + if len(name2) == 2: + self.db, self.name = name2 + elif len(name2) == 3: + self.db, self.name, self.cellid = name2 + else: + raise KeyError, repr(value) + ' parameter format error.' + else: + raise KeyError, repr(name) + ' not a valid parameter for this class.' + + if self.db and isinstance(self.db, basestring): + assert self.cursor, "Don't have a cursor" + self.db = webqtlDataset(self.db, self.cursor) + + #if self.db == None, not from a database + print("self.db is:", self.db, type(self.db)) + if self.db: + if self.db.type == "Temp": + self.cursor.execute(''' + SELECT + InbredSet.Name + FROM + InbredSet, Temp + WHERE + Temp.InbredSetId = InbredSet.Id AND + Temp.Name = "%s" + ''', self.name) + self.riset = self.cursor.fetchone()[0] + else: + self.riset = self.db.getRISet() + + # + # In ProbeSet, there are maybe several annotations match one sequence + # so we need use sequence(BlatSeq) as the identification, when we update + # one annotation, we update the others who match the sequence also. + # + # Hongqiang Li, 3/3/2008 + # + + #XZ, 05/08/2009: This block is not neccessary. We can add 'BlatSeq' into disfield. + # The variable self.sequence should be changed to self.BlatSeq + # It also should be changed in other places where it are used. + + if self.db: + if self.db.type == 'ProbeSet': + print("Doing ProbeSet Query") + query = ''' + SELECT + ProbeSet.BlatSeq + FROM + ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSet.Id=ProbeSetXRef.ProbeSetId and + ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and + ProbeSet.Name = %s and + ProbeSetFreeze.Name = %s + ''', (self.name, self.db.name) + print("query is:", query) + self.cursor.execute(*query) + self.sequence = self.cursor.fetchone()[0] + print("self.sequence is:", self.sequence) + + + def getName(self): + str = "" + if self.db and self.name: + str = "%s::%s" % (self.db, self.name) + if self.cellid: + str += "::" + self.cellid + else: + str = self.description + return str + + # + # when user enter a trait or GN generate a trait, user want show the name + # not the name that generated by GN randomly, the two follow function are + # used to give the real name and the database. displayName() will show the + # database also, getGivenName() just show the name. + # For other trait, displayName() as same as getName(), getGivenName() as + # same as self.name + # + # Hongqiang 11/29/07 + # + def getGivenName(self): + str = self.name + if self.db and self.name: + if self.db.type=='Temp': + self.cursor.execute('SELECT description FROM Temp WHERE Name=%s', self.name) + desc = self.cursor.fetchone()[0] + if desc.__contains__('PCA'): + desc = desc[desc.rindex(':')+1:].strip() + else: + desc = desc[:desc.index('entered')].strip() + str = desc + return str + + def displayName(self): + str = "" + if self.db and self.name: + if self.db.type=='Temp': + desc = self.description + if desc.__contains__('PCA'): + desc = desc[desc.rindex(':')+1:].strip() + else: + desc = desc[:desc.index('entered')].strip() + str = "%s::%s" % (self.db, desc) + else: + str = "%s::%s" % (self.db, self.name) + if self.cellid: + str += "::" + self.cellid + else: + str = self.description + + return str + + + #def __str__(self): + # #return "%s %s" % (self.getName(), self.riset) + # return self.getName() + __str__ = getName + __repr__ = __str__ + + def exportData(self, strainlist, type="val"): + """ + export data according to strainlist + mostly used in calculating correlation + """ + result = [] + for strain in strainlist: + if self.data.has_key(strain): + if type=='val': + result.append(self.data[strain].val) + elif type=='var': + result.append(self.data[strain].var) + elif type=='N': + result.append(self.data[strain].N) + else: + raise KeyError, `type`+' type is incorrect.' + else: + result.append(None) + return result + + def exportInformative(self, incVar=0): + """ + export informative strain + mostly used in qtl regression + """ + strains = [] + vals = [] + vars = [] + for strain, value in self.data.items(): + if value.val != None: + if not incVar or value.var != None: + strains.append(strain) + vals.append(value.val) + vars.append(value.var) + return strains, vals, vars + + + # + # In ProbeSet, there are maybe several annotations match one sequence + # so we need use sequence(BlatSeq) as the identification, when we update + # one annotation, we update the others who match the sequence also. + # + # Hongqiang Li, 3/3/2008 + # + def getSequence(self): + assert self.cursor + if self.db.type == 'ProbeSet': + self.cursor.execute(''' + SELECT + ProbeSet.BlatSeq + FROM + ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSet.Id=ProbeSetXRef.ProbeSetId and + ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and + ProbeSet.Name = %s + ProbeSetFreeze.Name = %s + ''', self.name, self.db.name) + #self.cursor.execute(query) + results = self.fetchone() + + return results[0] + + + + def retrieveData(self, strainlist=[]): + assert self.db and self.cursor + + if self.db.type == 'Temp': + query = ''' + SELECT + Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id + FROM + TempData, Temp, Strain + WHERE + TempData.StrainId = Strain.Id AND + TempData.Id = Temp.DataId AND + Temp.name = '%s' + Order BY + Strain.Name + ''' % self.name + #XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE + elif self.db.type == 'Publish': + query = ''' + SELECT + Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id + FROM + (PublishData, Strain, PublishXRef, PublishFreeze) + left join PublishSE on + (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId) + left join NStrain on + (NStrain.DataId = PublishData.Id AND + NStrain.StrainId = PublishData.StrainId) + WHERE + PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND + PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id + Order BY + Strain.Name + ''' % (self.name, self.db.id) + + #XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE + elif self.cellid: + #Probe Data + query = ''' + SELECT + Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id + FROM + (ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, + Strain, Probe, ProbeSet) + left join ProbeSE on + (ProbeSE.DataId = ProbeData.Id AND ProbeSE.StrainId = ProbeData.StrainId) + WHERE + Probe.Name = '%s' AND ProbeSet.Name = '%s' AND + Probe.ProbeSetId = ProbeSet.Id AND + ProbeXRef.ProbeId = Probe.Id AND + ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND + ProbeSetFreeze.Name = '%s' AND + ProbeXRef.DataId = ProbeData.Id AND + ProbeData.StrainId = Strain.Id + Order BY + Strain.Name + ''' % (self.cellid, self.name, self.db.name) + #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE + elif self.db.type == 'ProbeSet': + #ProbeSet Data + query = ''' + SELECT + Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id + FROM + (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef) + left join ProbeSetSE on + (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) + WHERE + ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetFreeze.Name = '%s' AND + ProbeSetXRef.DataId = ProbeSetData.Id AND + ProbeSetData.StrainId = Strain.Id + Order BY + Strain.Name + ''' % (self.name, self.db.name) + #XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE + else: + #Geno Data + #XZ: The SpeciesId is not necessary, but it's nice to keep it to speed up database search. + query = ''' + SELECT + Strain.Name, GenoData.value, GenoSE.error, GenoData.Id + FROM + (GenoData, GenoFreeze, Strain, Geno, GenoXRef) + left join GenoSE on + (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) + WHERE + Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND + GenoXRef.GenoFreezeId = GenoFreeze.Id AND + GenoFreeze.Name = '%s' AND + GenoXRef.DataId = GenoData.Id AND + GenoData.StrainId = Strain.Id + Order BY + Strain.Name + ''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.db.riset), self.name, self.db.name) + + + self.cursor.execute(query) + results = self.cursor.fetchall() + self.data.clear() + if results: + self.mysqlid = results[0][-1] + if strainlist: + for item in results: + if item[0] in strainlist: + val = item[1] + if val != None: + var = item[2] + ndata = None + if self.db.type in ('Publish', 'Temp'): + ndata = item[3] + self.data[item[0]] = webqtlCaseData(val, var, ndata) + #end for + else: + for item in results: + val = item[1] + if val != None: + var = item[2] + ndata = None + if self.db.type in ('Publish', 'Temp'): + ndata = item[3] + self.data[item[0]] = webqtlCaseData(val, var, ndata) + #end for + #end if + else: + pass + + def keys(self): + return self.__dict__.keys() + + def has_key(self, key): + return self.__dict__.has_key(key) + + def items(self): + return self.__dict__.items() + + def retrieveInfo(self, QTL = None): + assert self.db and self.cursor + if self.db.type == 'Publish': + #self.db.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\ + # 'Abstract', 'Journal','Volume','Pages','Month','Year','Sequence',\ + # 'Units', 'comments'] + query = ''' + SELECT + PublishXRef.Id, Publication.PubMed_ID, + Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, + Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, + Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, + Publication.Authors, Publication.Title, Publication.Abstract, + Publication.Journal, Publication.Volume, Publication.Pages, + Publication.Month, Publication.Year, PublishXRef.Sequence, + Phenotype.Units, PublishXRef.comments + FROM + PublishXRef, Publication, Phenotype, PublishFreeze + WHERE + PublishXRef.Id = %s AND + Phenotype.Id = PublishXRef.PhenotypeId AND + Publication.Id = PublishXRef.PublicationId AND + PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + PublishFreeze.Id =%s + ''' % (self.name, self.db.id) + #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name + #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. + elif self.db.type == 'ProbeSet': + disfieldString = string.join(self.db.disfield,',ProbeSet.') + disfieldString = 'ProbeSet.' + disfieldString + query = """ + SELECT %s + FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetFreeze.Name = '%s' AND + ProbeSet.Name = '%s' + """ % (disfieldString, self.db.name, self.name) + #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name + # to avoid the problem of same marker name from different species. + elif self.db.type == 'Geno': + disfieldString = string.join(self.db.disfield,',Geno.') + disfieldString = 'Geno.' + disfieldString + query = """ + SELECT %s + FROM Geno, GenoFreeze, GenoXRef + WHERE + GenoXRef.GenoFreezeId = GenoFreeze.Id AND + GenoXRef.GenoId = Geno.Id AND + GenoFreeze.Name = '%s' AND + Geno.Name = '%s' + """ % (disfieldString, self.db.name, self.name) + else: #Temp type + query = 'SELECT %s FROM %s WHERE Name = "%s"' % \ + (string.join(self.db.disfield,','), self.db.type, self.name) + + + self.cursor.execute(query) + traitInfo = self.cursor.fetchone() + if traitInfo: + self.haveinfo = 1 + + #XZ: assign SQL query result to trait attributes. + for i, field in enumerate(self.db.disfield): + setattr(self, field, traitInfo[i]) + + if self.db.type == 'Publish': + self.confidential = 0 + if self.pre_publication_description and not self.pubmed_id: + self.confidential = 1 + + self.homologeneid = None + if self.db.type == 'ProbeSet' and self.riset and self.geneid: + #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number. + #XZ: So I have to test if geneid is number before execute the query. + #XZ: The geneid values in database should be cleaned up. + try: + junk = float(self.geneid) + geneidIsNumber = 1 + except: + geneidIsNumber = 0 + + if geneidIsNumber: + query = """ + SELECT + HomologeneId + FROM + Homologene, Species, InbredSet + WHERE + Homologene.GeneId =%s AND + InbredSet.Name = '%s' AND + InbredSet.SpeciesId = Species.Id AND + Species.TaxonomyId = Homologene.TaxonomyId + """ % (self.geneid, self.riset) + self.cursor.execute(query) + result = self.cursor.fetchone() + else: + result = None + + if result: + self.homologeneid = result[0] + + if QTL: + if self.db.type == 'ProbeSet' and not self.cellid: + query = ''' + SELECT + ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean + FROM + ProbeSetXRef, ProbeSet + WHERE + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSet.Name = "%s" AND + ProbeSetXRef.ProbeSetFreezeId =%s + ''' % (self.name, self.db.id) + self.cursor.execute(query) + traitQTL = self.cursor.fetchone() + if traitQTL: + self.locus, self.lrs, self.pvalue, self.mean = traitQTL + else: + self.locus = self.lrs = self.pvalue = self.mean = "" + if self.db.type == 'Publish': + query = ''' + SELECT + PublishXRef.Locus, PublishXRef.LRS + FROM + PublishXRef, PublishFreeze + WHERE + PublishXRef.Id = %s AND + PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + PublishFreeze.Id =%s + ''' % (self.name, self.db.id) + self.cursor.execute(query) + traitQTL = self.cursor.fetchone() + if traitQTL: + self.locus, self.lrs = traitQTL + else: + self.locus = self.lrs = "" + else: + raise KeyError, `self.name`+' information is not found in the database.' + + def genHTML(self, formName = "", dispFromDatabase=0, privilege="guest", userName="Guest", authorized_users=""): + if not self.haveinfo: + self.retrieveInfo() + + if self.db.type == 'Publish': + PubMedLink = "" + if self.pubmed_id: + PubMedLink = HT.Href(text="PubMed %d : " % self.pubmed_id, + target = "_blank", url = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id) + else: + PubMedLink = HT.Span("Unpublished : ", Class="fs15") + + if formName: + setDescription2 = HT.Href(url="javascript:showDatabase3('%s','%s','%s','')" % + (formName, self.db.name, self.name), Class = "fs14") + else: + setDescription2 = HT.Href(url="javascript:showDatabase2('%s','%s','')" % + (self.db.name,self.name), Class = "fs14") + + if self.confidential and not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=privilege, userName=userName, authorized_users=authorized_users): + setDescription2.append('RecordID/%s - %s' % (self.name, self.pre_publication_description)) + else: + setDescription2.append('RecordID/%s - %s' % (self.name, self.post_publication_description)) + + #XZ 03/26/2011: Xiaodong comment out the following two lins as Rob asked. Need to check with Rob why in PublishXRef table, there are few row whose Sequence > 1. + #if self.sequence > 1: + # setDescription2.append(' btach %d' % self.sequence) + if self.authors: + a1 = string.split(self.authors,',')[0] + while a1[0] == '"' or a1[0] == "'" : + a1 = a1[1:] + setDescription2.append(' by ') + setDescription2.append(HT.Italic('%s, and colleagues' % a1)) + setDescription = HT.Span(PubMedLink, setDescription2) + + elif self.db.type == 'Temp': + setDescription = HT.Href(text="%s" % (self.description),url="javascript:showDatabase2\ + ('%s','%s','')" % (self.db.name,self.name), Class = "fs14") + setDescription = HT.Span(setDescription) + + elif self.db.type == 'Geno': # Genome DB only available for single search + if formName: + setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\ + '%2.3f' % self.mb),url="javascript:showDatabase3('%s','%s','%s','')" % \ + (formName, self.db.name, self.name), Class = "fs14") + else: + setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\ + '%2.3f' % self.mb),url="javascript:showDatabase2('%s','%s','')" % \ + (self.db.name,self.name), Class = "fs14") + + setDescription = HT.Span(setDescription) + + else: + if self.cellid: + if formName: + setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name, self.cellid),url=\ + "javascript:showDatabase3('%s','%s','%s','%s')" % (formName, self.db.name,self.name,self.cellid), \ + Class = "fs14") + else: + setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name,self.cellid),url=\ + "javascript:showDatabase2('%s','%s','%s')" % (self.db.name,self.name,self.cellid), \ + Class = "fs14") + else: + if formName: + setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\ + "javascript:showDatabase3('%s','%s','%s','')" % (formName, self.db.name,self.name), \ + Class = "fs14") + else: + setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\ + "javascript:showDatabase2('%s','%s','')" % (self.db.name,self.name), \ + Class = "fs14") + if self.symbol and self.chr and self.mb: + setDescription.append(' [') + setDescription.append(HT.Italic('%s' % self.symbol,Class="cdg fwb")) + setDescription.append(' on Chr %s @ %s Mb]' % (self.chr,self.mb)) + if self.description: + setDescription.append(': %s' % self.description) + if self.probe_target_description: + setDescription.append('; %s' % self.probe_target_description) + setDescription = HT.Span(setDescription) + + if self.db.type != 'Temp' and dispFromDatabase: + setDescription.append( ' --- FROM : ') + setDescription.append(self.db.genHTML(Class='cori')) + return setDescription diff --git a/wqflask/basicStatistics/BasicStatisticsFunctions.py b/wqflask/basicStatistics/BasicStatisticsFunctions.py index 5cbbb145..285addae 100755 --- a/wqflask/basicStatistics/BasicStatisticsFunctions.py +++ b/wqflask/basicStatistics/BasicStatisticsFunctions.py @@ -13,162 +13,162 @@ from dbFunction import webqtlDatabaseFunction def basicStatsTable(vals, trait_type=None, cellid=None, heritability=None): - valsOnly = [] - dataXZ = vals[:] - for i in range(len(dataXZ)): - valsOnly.append(dataXZ[i][1]) - - traitmean, traitmedian, traitvar, traitstdev, traitsem, N = reaper.anova(valsOnly) #ZS: Should convert this from reaper to R in the future - - tbl = HT.TableLite(cellpadding=20, cellspacing=0) - dataXZ = vals[:] - dataXZ.sort(webqtlUtil.cmpOrder) - tbl.append(HT.TR(HT.TD("Statistic",align="left", Class="fs14 fwb ffl b1 cw cbrb", width = 180), - HT.TD("Value", align="right", Class="fs14 fwb ffl b1 cw cbrb", width = 60))) - tbl.append(HT.TR(HT.TD("N of Samples",align="left", Class="fs13 b1 cbw c222"), - HT.TD(N,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) - tbl.append(HT.TR(HT.TD("Mean",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.3f" % traitmean,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) - tbl.append(HT.TR(HT.TD("Median",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.3f" % traitmedian,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) - #tbl.append(HT.TR(HT.TD("Variance",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), - # HT.TD("%2.3f" % traitvar,nowrap="yes",align="left", Class="fs13 b1 cbw c222"))) - tbl.append(HT.TR(HT.TD("Standard Error (SE)",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.3f" % traitsem,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) - tbl.append(HT.TR(HT.TD("Standard Deviation (SD)", align="left", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.3f" % traitstdev,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) - tbl.append(HT.TR(HT.TD("Minimum", align="left", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%s" % dataXZ[0][1],nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) - tbl.append(HT.TR(HT.TD("Maximum", align="left", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%s" % dataXZ[-1][1],nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) - if (trait_type != None and trait_type == 'ProbeSet'): - #IRQuest = HT.Href(text="Interquartile Range", url=webqtlConfig.glossaryfile +"#Interquartile",target="_blank", Class="fs14") - #IRQuest.append(HT.BR()) - #IRQuest.append(" (fold difference)") - tbl.append(HT.TR(HT.TD("Range (log2)",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.3f" % (dataXZ[-1][1]-dataXZ[0][1]),nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) - tbl.append(HT.TR(HT.TD(HT.Span("Range (fold)"),align="left", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.2f" % pow(2.0,(dataXZ[-1][1]-dataXZ[0][1])), nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) - tbl.append(HT.TR(HT.TD(HT.Span(HT.Href(url="/glossary.html#Interquartile", target="_blank", text="Interquartile Range", Class="non_bold")), align="left", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.2f" % pow(2.0,(dataXZ[int((N-1)*3.0/4.0)][1]-dataXZ[int((N-1)/4.0)][1])), nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) - - #XZ, 04/01/2009: don't try to get H2 value for probe. - if cellid: - pass - else: - if heritability: - tbl.append(HT.TR(HT.TD(HT.Span("Heritability"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"),HT.TD("%s" % heritability, nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - else: - pass - # Lei Yan - # 2008/12/19 - - return tbl + valsOnly = [] + dataXZ = vals[:] + for i in range(len(dataXZ)): + valsOnly.append(dataXZ[i][1]) + + traitmean, traitmedian, traitvar, traitstdev, traitsem, N = reaper.anova(valsOnly) #ZS: Should convert this from reaper to R in the future + + tbl = HT.TableLite(cellpadding=20, cellspacing=0) + dataXZ = vals[:] + dataXZ.sort(webqtlUtil.cmpOrder) + tbl.append(HT.TR(HT.TD("Statistic",align="left", Class="fs14 fwb ffl b1 cw cbrb", width = 180), + HT.TD("Value", align="right", Class="fs14 fwb ffl b1 cw cbrb", width = 60))) + tbl.append(HT.TR(HT.TD("N of Samples",align="left", Class="fs13 b1 cbw c222"), + HT.TD(N,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD("Mean",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitmean,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD("Median",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitmedian,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + #tbl.append(HT.TR(HT.TD("Variance",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + # HT.TD("%2.3f" % traitvar,nowrap="yes",align="left", Class="fs13 b1 cbw c222"))) + tbl.append(HT.TR(HT.TD("Standard Error (SE)",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitsem,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD("Standard Deviation (SD)", align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitstdev,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD("Minimum", align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%s" % dataXZ[0][1],nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD("Maximum", align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%s" % dataXZ[-1][1],nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + if (trait_type != None and trait_type == 'ProbeSet'): + #IRQuest = HT.Href(text="Interquartile Range", url=webqtlConfig.glossaryfile +"#Interquartile",target="_blank", Class="fs14") + #IRQuest.append(HT.BR()) + #IRQuest.append(" (fold difference)") + tbl.append(HT.TR(HT.TD("Range (log2)",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % (dataXZ[-1][1]-dataXZ[0][1]),nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD(HT.Span("Range (fold)"),align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.2f" % pow(2.0,(dataXZ[-1][1]-dataXZ[0][1])), nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD(HT.Span(HT.Href(url="/glossary.html#Interquartile", target="_blank", text="Interquartile Range", Class="non_bold")), align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.2f" % pow(2.0,(dataXZ[int((N-1)*3.0/4.0)][1]-dataXZ[int((N-1)/4.0)][1])), nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + + #XZ, 04/01/2009: don't try to get H2 value for probe. + if cellid: + pass + else: + if heritability: + tbl.append(HT.TR(HT.TD(HT.Span("Heritability"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"),HT.TD("%s" % heritability, nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + else: + pass + # Lei Yan + # 2008/12/19 + + return tbl def plotNormalProbability(vals=None, RISet='', title=None, showstrains=0, specialStrains=[None], size=(750,500)): - dataXZ = vals[:] - dataXZ.sort(webqtlUtil.cmpOrder) - dataLabel = [] - dataX = map(lambda X: X[1], dataXZ) + dataXZ = vals[:] + dataXZ.sort(webqtlUtil.cmpOrder) + dataLabel = [] + dataX = map(lambda X: X[1], dataXZ) - showLabel = showstrains - if len(dataXZ) > 50: - showLabel = 0 - for item in dataXZ: - strainName = webqtlUtil.genShortStrainName(RISet=RISet, input_strainName=item[0]) - dataLabel.append(strainName) + showLabel = showstrains + if len(dataXZ) > 50: + showLabel = 0 + for item in dataXZ: + strainName = webqtlUtil.genShortStrainName(RISet=RISet, input_strainName=item[0]) + dataLabel.append(strainName) - dataY=Plot.U(len(dataX)) - dataZ=map(Plot.inverseCumul,dataY) - c = pid.PILCanvas(size=(750,500)) - Plot.plotXY(c, dataZ, dataX, dataLabel = dataLabel, XLabel='Expected Z score', connectdot=0, YLabel='Trait value', title=title, specialCases=specialStrains, showLabel = showLabel) + dataY=Plot.U(len(dataX)) + dataZ=map(Plot.inverseCumul,dataY) + c = pid.PILCanvas(size=(750,500)) + Plot.plotXY(c, dataZ, dataX, dataLabel = dataLabel, XLabel='Expected Z score', connectdot=0, YLabel='Trait value', title=title, specialCases=specialStrains, showLabel = showLabel) - filename= webqtlUtil.genRandStr("nP_") - c.save(webqtlConfig.IMGDIR+filename, format='gif') + filename= webqtlUtil.genRandStr("nP_") + c.save(webqtlConfig.IMGDIR+filename, format='gif') - img=HT.Image('/image/'+filename+'.gif',border=0) + img=HT.Image('/image/'+filename+'.gif',border=0) - return img + return img def plotBoxPlot(vals): - valsOnly = [] - dataXZ = vals[:] - for i in range(len(dataXZ)): - valsOnly.append(dataXZ[i][1]) + valsOnly = [] + dataXZ = vals[:] + for i in range(len(dataXZ)): + valsOnly.append(dataXZ[i][1]) - plotHeight = 320 - plotWidth = 220 - xLeftOffset = 60 - xRightOffset = 40 - yTopOffset = 40 - yBottomOffset = 60 + plotHeight = 320 + plotWidth = 220 + xLeftOffset = 60 + xRightOffset = 40 + yTopOffset = 40 + yBottomOffset = 60 - canvasHeight = plotHeight + yTopOffset + yBottomOffset - canvasWidth = plotWidth + xLeftOffset + xRightOffset - canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight)) - XXX = [('', valsOnly[:])] + canvasHeight = plotHeight + yTopOffset + yBottomOffset + canvasWidth = plotWidth + xLeftOffset + xRightOffset + canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight)) + XXX = [('', valsOnly[:])] - Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel= "Trait") - filename= webqtlUtil.genRandStr("Box_") - canvas.save(webqtlConfig.IMGDIR+filename, format='gif') - img=HT.Image('/image/'+filename+'.gif',border=0) + Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel= "Trait") + filename= webqtlUtil.genRandStr("Box_") + canvas.save(webqtlConfig.IMGDIR+filename, format='gif') + img=HT.Image('/image/'+filename+'.gif',border=0) - plotLink = HT.Span("More about ", HT.Href(text="Box Plots", url="http://davidmlane.com/hyperstat/A37797.html", target="_blank", Class="fs13")) + plotLink = HT.Span("More about ", HT.Href(text="Box Plots", url="http://davidmlane.com/hyperstat/A37797.html", target="_blank", Class="fs13")) - return img, plotLink + return img, plotLink def plotBarGraph(identification='', RISet='', vals=None, type="name"): - this_identification = "unnamed trait" - if identification: - this_identification = identification - - if type=="rank": - dataXZ = vals[:] - dataXZ.sort(webqtlUtil.cmpOrder) - title='%s' % this_identification - else: - dataXZ = vals[:] - title='%s' % this_identification - - tvals = [] - tnames = [] - tvars = [] - for i in range(len(dataXZ)): - tvals.append(dataXZ[i][1]) - tnames.append(webqtlUtil.genShortStrainName(RISet=RISet, input_strainName=dataXZ[i][0])) - tvars.append(dataXZ[i][2]) - nnStrain = len(tnames) - - sLabel = 1 - - ###determine bar width and space width - if nnStrain < 20: - sw = 4 - elif nnStrain < 40: - sw = 3 - else: - sw = 2 - - ### 700 is the default plot width minus Xoffsets for 40 strains - defaultWidth = 650 - if nnStrain > 40: - defaultWidth += (nnStrain-40)*10 - defaultOffset = 100 - bw = int(0.5+(defaultWidth - (nnStrain-1.0)*sw)/nnStrain) - if bw < 10: - bw = 10 - - plotWidth = (nnStrain-1)*sw + nnStrain*bw + defaultOffset - plotHeight = 500 - #print [plotWidth, plotHeight, bw, sw, nnStrain] - c = pid.PILCanvas(size=(plotWidth,plotHeight)) - Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title=title, sLabel = sLabel, barSpace = sw) - - filename= webqtlUtil.genRandStr("Bar_") - c.save(webqtlConfig.IMGDIR+filename, format='gif') - img=HT.Image('/image/'+filename+'.gif',border=0) - - return img + this_identification = "unnamed trait" + if identification: + this_identification = identification + + if type=="rank": + dataXZ = vals[:] + dataXZ.sort(webqtlUtil.cmpOrder) + title='%s' % this_identification + else: + dataXZ = vals[:] + title='%s' % this_identification + + tvals = [] + tnames = [] + tvars = [] + for i in range(len(dataXZ)): + tvals.append(dataXZ[i][1]) + tnames.append(webqtlUtil.genShortStrainName(RISet=RISet, input_strainName=dataXZ[i][0])) + tvars.append(dataXZ[i][2]) + nnStrain = len(tnames) + + sLabel = 1 + + ###determine bar width and space width + if nnStrain < 20: + sw = 4 + elif nnStrain < 40: + sw = 3 + else: + sw = 2 + + ### 700 is the default plot width minus Xoffsets for 40 strains + defaultWidth = 650 + if nnStrain > 40: + defaultWidth += (nnStrain-40)*10 + defaultOffset = 100 + bw = int(0.5+(defaultWidth - (nnStrain-1.0)*sw)/nnStrain) + if bw < 10: + bw = 10 + + plotWidth = (nnStrain-1)*sw + nnStrain*bw + defaultOffset + plotHeight = 500 + #print [plotWidth, plotHeight, bw, sw, nnStrain] + c = pid.PILCanvas(size=(plotWidth,plotHeight)) + Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title=title, sLabel = sLabel, barSpace = sw) + + filename= webqtlUtil.genRandStr("Bar_") + c.save(webqtlConfig.IMGDIR+filename, format='gif') + img=HT.Image('/image/'+filename+'.gif',border=0) + + return img diff --git a/wqflask/basicStatistics/BasicStatisticsPage_alpha.py b/wqflask/basicStatistics/BasicStatisticsPage_alpha.py index 4ba9d54a..365143db 100755 --- a/wqflask/basicStatistics/BasicStatisticsPage_alpha.py +++ b/wqflask/basicStatistics/BasicStatisticsPage_alpha.py @@ -43,306 +43,302 @@ from dbFunction import webqtlDatabaseFunction class BasicStatisticsPage_alpha(templatePage): - plotMinInformative = 4 - - def __init__(self, fd): - - templatePage.__init__(self, fd) - - if not fd.genotype: - fd.readGenotype() - strainlist2 = fd.strainlist - - if fd.allstrainlist: - strainlist2 = fd.allstrainlist - - fd.readData(strainlist2) - - specialStrains = [] - setStrains = [] - for item in strainlist2: - if item not in fd.strainlist and item.find('F1') < 0: - specialStrains.append(item) - else: - setStrains.append(item) - specialStrains.sort() - #So called MDP Panel - if specialStrains: - specialStrains = fd.f1list+fd.parlist+specialStrains - - self.plotType = fd.formdata.getvalue('ptype', '0') - plotStrains = strainlist2 - if specialStrains: - if self.plotType == '1': - plotStrains = setStrains - if self.plotType == '2': - plotStrains = specialStrains - - self.dict['title'] = 'Basic Statistics' - if not self.openMysql(): - return - - self.showstrains = 1 - self.identification = "unnamed trait" - - self.fullname = fd.formdata.getvalue('fullname', '') - if self.fullname: - self.Trait = webqtlTrait(fullname=self.fullname, cursor=self.cursor) - self.Trait.retrieveInfo() - else: - self.Trait = None - - if fd.identification: - self.identification = fd.identification - self.dict['title'] = self.identification + ' / '+self.dict['title'] - TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') - - ##should not display Variance, but cannot convert Variance to SE - #print plotStrains, fd.allTraitData.keys() - if len(fd.allTraitData) > 0: - vals=[] - InformData = [] - for _strain in plotStrains: - if fd.allTraitData.has_key(_strain): - _val, _var = fd.allTraitData[_strain].val, fd.allTraitData[_strain].var - if _val != None: - vals.append([_strain, _val, _var]) - InformData.append(_val) - - if len(vals) >= self.plotMinInformative: - supertable2 = HT.TableLite(border=0, cellspacing=0, cellpadding=5,width="800") - - staIntro1 = HT.Paragraph("The table and plots below list the basic statistical analysis result of trait",HT.Strong(" %s" % self.identification)) - - ##### - #anova - ##### - traitmean, traitmedian, traitvar, traitstdev, traitsem, N = reaper.anova(InformData) - TDStatis = HT.TD(width="360", valign="top") - tbl2 = HT.TableLite(cellpadding=5, cellspacing=0, Class="collap") - dataXZ = vals[:] - dataXZ.sort(self.cmpValue) - tbl2.append(HT.TR(HT.TD("Statistic",align="center", Class="fs14 fwb ffl b1 cw cbrb", width = 200), - HT.TD("Value", align="center", Class="fs14 fwb ffl b1 cw cbrb", width = 140))) - tbl2.append(HT.TR(HT.TD("N of Cases",align="center", Class="fs13 b1 cbw c222"), - HT.TD(N,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - tbl2.append(HT.TR(HT.TD("Mean",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.3f" % traitmean,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - tbl2.append(HT.TR(HT.TD("Median",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.3f" % traitmedian,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - #tbl2.append(HT.TR(HT.TD("Variance",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), - # HT.TD("%2.3f" % traitvar,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - tbl2.append(HT.TR(HT.TD("SEM",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.3f" % traitsem,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - tbl2.append(HT.TR(HT.TD("SD",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.3f" % traitstdev,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - tbl2.append(HT.TR(HT.TD("Minimum",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%s" % dataXZ[0][1],nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - tbl2.append(HT.TR(HT.TD("Maximum",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%s" % dataXZ[-1][1],nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - if self.Trait and self.Trait.db.type == 'ProbeSet': - #IRQuest = HT.Href(text="Interquartile Range", url=webqtlConfig.glossaryfile +"#Interquartile",target="_blank", Class="fs14") - #IRQuest.append(HT.BR()) - #IRQuest.append(" (fold difference)") - tbl2.append(HT.TR(HT.TD("Range (log2)",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.3f" % (dataXZ[-1][1]-dataXZ[0][1]),nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - tbl2.append(HT.TR(HT.TD(HT.Span("Range (fold)"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.2f" % pow(2.0,(dataXZ[-1][1]-dataXZ[0][1])), nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - tbl2.append(HT.TR(HT.TD(HT.Span("Quartile Range",HT.BR()," (fold difference)"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"), - HT.TD("%2.2f" % pow(2.0,(dataXZ[int((N-1)*3.0/4.0)][1]-dataXZ[int((N-1)/4.0)][1])), nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - - # (Lei Yan) - # 2008/12/19 - self.Trait.retrieveData() - #XZ, 04/01/2009: don't try to get H2 value for probe. - if self.Trait.cellid: - pass - else: - self.cursor.execute("SELECT DataId, h2 from ProbeSetXRef WHERE DataId = %d" % self.Trait.mysqlid) - dataid, heritability = self.cursor.fetchone() - if heritability: - tbl2.append(HT.TR(HT.TD(HT.Span("Heritability"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"),HT.TD("%s" % heritability, nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - else: - tbl2.append(HT.TR(HT.TD(HT.Span("Heritability"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"),HT.TD("NaN", nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) - - # Lei Yan - # 2008/12/19 - - TDStatis.append(tbl2) - - plotHeight = 220 - plotWidth = 120 - xLeftOffset = 60 - xRightOffset = 25 - yTopOffset = 20 - yBottomOffset = 53 - - canvasHeight = plotHeight + yTopOffset + yBottomOffset - canvasWidth = plotWidth + xLeftOffset + xRightOffset - canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight)) - XXX = [('', InformData[:])] - - Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel= "Trait") - filename= webqtlUtil.genRandStr("Box_") - canvas.save(webqtlConfig.IMGDIR+filename, format='gif') - img=HT.Image('/image/'+filename+'.gif',border=0) - - #supertable2.append(HT.TR(HT.TD(staIntro1, colspan=3 ))) - tb = HT.TableLite(border=0, cellspacing=0, cellpadding=0) - tb.append(HT.TR(HT.TD(img, align="left", style="border: 1px solid #999999; padding:0px;"))) - supertable2.append(HT.TR(TDStatis, HT.TD(tb))) - - dataXZ = vals[:] - tvals = [] - tnames = [] - tvars = [] - for i in range(len(dataXZ)): - tvals.append(dataXZ[i][1]) - tnames.append(webqtlUtil.genShortStrainName(fd, dataXZ[i][0])) - tvars.append(dataXZ[i][2]) - nnStrain = len(tnames) - - sLabel = 1 - - ###determine bar width and space width - if nnStrain < 20: - sw = 4 - elif nnStrain < 40: - sw = 3 - else: - sw = 2 - - ### 700 is the default plot width minus Xoffsets for 40 strains - defaultWidth = 650 - if nnStrain > 40: - defaultWidth += (nnStrain-40)*10 - defaultOffset = 100 - bw = int(0.5+(defaultWidth - (nnStrain-1.0)*sw)/nnStrain) - if bw < 10: - bw = 10 - - plotWidth = (nnStrain-1)*sw + nnStrain*bw + defaultOffset - plotHeight = 500 - #print [plotWidth, plotHeight, bw, sw, nnStrain] - c = pid.PILCanvas(size=(plotWidth,plotHeight)) - Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title='%s by Case (sorted by name)' % self.identification, sLabel = sLabel, barSpace = sw) - - filename= webqtlUtil.genRandStr("Bar_") - c.save(webqtlConfig.IMGDIR+filename, format='gif') - img0=HT.Image('/image/'+filename+'.gif',border=0) - - dataXZ = vals[:] - dataXZ.sort(self.cmpValue) - tvals = [] - tnames = [] - tvars = [] - for i in range(len(dataXZ)): - tvals.append(dataXZ[i][1]) - tnames.append(webqtlUtil.genShortStrainName(fd, dataXZ[i][0])) - tvars.append(dataXZ[i][2]) - - c = pid.PILCanvas(size=(plotWidth,plotHeight)) - Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title='%s by Case (ranked)' % self.identification, sLabel = sLabel, barSpace = sw) - - filename= webqtlUtil.genRandStr("Bar_") - c.save(webqtlConfig.IMGDIR+filename, format='gif') - img1=HT.Image('/image/'+filename+'.gif',border=0) - - # Lei Yan - # 05/18/2009 - # report - - title = HT.Paragraph('REPORT on the variation of Shh (or PCA Composite Trait XXXX) (sonic hedgehog) in the (insert Data set name) of (insert Species informal name, e.g., Mouse, Rat, Human, Barley, Arabidopsis)', Class="title") - header = HT.Paragraph('''This report was generated by GeneNetwork on May 11, 2009, at 11.20 AM using the Basic Statistics module (v 1.0) and data from the Hippocampus Consortium M430v2 (Jun06) PDNN data set. For more details and updates on this data set please link to URL:get Basic Statistics''') - hr = HT.HR() - p1 = HT.Paragraph('''Trait values for Shh were taken from the (insert Database name, Hippocampus Consortium M430v2 (Jun06) PDNN). GeneNetwork contains data for NN (e.g., 99) cases. In general, data are averages for each case. A summary of mean, median, and the range of these data are provided in Table 1 and in the box plot (Figure 1). Data for individual cases are provided in Figure 2A and 2B, often with error bars (SEM). ''') - p2 = HT.Paragraph('''Trait values for Shh range 5.1-fold: from a low of 8.2 (please round value) in 129S1/SvImJ to a high of 10.6 (please round value) in BXD9. The interquartile range (the difference between values closest to the 25% and 75% levels) is a more modest 1.8-fold. The mean value is XX. ''') - t1 = HT.Paragraph('''Table 1. Summary of Shh data from the Hippocampus Consortium M430v2 (june06) PDNN data set''') - f1 = HT.Paragraph('''Figure 1. ''') - f1.append(HT.Href(text="Box plot", url="http://davidmlane.com/hyperstat/A37797.html", target="_blank", Class="fs14")) - f1.append(HT.Text(''' of Shh data from the Hippocampus Consortium M430v2 (june06) PDNN data set''')) - f2A = HT.Paragraph('''Figure 2A: Bar chart of Shh data ordered by case from the Hippocampus Consortium M430v2 (june06) PDNN data set''') - f2B = HT.Paragraph('''Figure 2B: Bar chart of Shh values ordered by from the Hippocampus Consortium M430v2 (june06) PDNN data set''') - TD_LR.append(HT.Blockquote(title, HT.P(), header, hr, p1, HT.P(), p2, HT.P(), supertable2, t1, f1, HT.P(), img0, f2A, HT.P(), img1, f2B)) - self.dict['body'] = str(TD_LR) - else: - heading = "Basic Statistics" - detail = ['Fewer than %d case data were entered for %s data set. No statitical analysis has been attempted.' % (self.plotMinInformative, fd.RISet)] - self.error(heading=heading,detail=detail) - return - else: - heading = "Basic Statistics" - detail = ['Empty data set, please check your data.'] - self.error(heading=heading,detail=detail) - return - - def traitInfo(self, fd, specialStrains = None): - species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) - heading2 = HT.Paragraph(HT.Strong('Population: '), "%s %s" % (species.title(), fd.RISet) , HT.BR()) - if self.Trait: - trait_url = HT.Href(text=self.Trait.name, url = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + \ - "?FormID=showDatabase&incparentsf1=1&database=%s&ProbeSetID=%s" % (self.Trait.db.name, self.Trait.name), \ - target='_blank', Class="fs13 fwn") - heading2.append(HT.Strong("Database: "), - HT.Href(text=self.Trait.db.fullname, url = webqtlConfig.INFOPAGEHREF % self.Trait.db.name , - target='_blank',Class="fs13 fwn"),HT.BR()) - if self.Trait.db.type == 'ProbeSet': - heading2.append(HT.Strong('Trait ID: '), trait_url, HT.BR(), - HT.Strong("Gene Symbol: "), HT.Italic('%s' % self.Trait.symbol,id="green"),HT.BR()) - if self.Trait.chr and self.Trait.mb: - heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (self.Trait.chr, self.Trait.mb)) - elif self.Trait.db.type == 'Geno': - heading2.append(HT.Strong('Locus : '), trait_url, HT.BR()) - #heading2.append(HT.Strong("Gene Symbol: "), HT.Italic('%s' % self.Trait.Symbol,id="green"),HT.BR()) - if self.Trait.chr and self.Trait.mb: - heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (self.Trait.chr, self.Trait.mb)) - elif self.Trait.db.type == 'Publish': - heading2.append(HT.Strong('Record ID: '), trait_url, HT.BR()) - heading2.append(HT.Strong('Phenotype: '), self.Trait.phenotype, HT.BR()) - heading2.append(HT.Strong('Author: '), self.Trait.authors, HT.BR()) - elif self.Trait.db.type == 'Temp': - heading2.append(HT.Strong('Description: '), self.Trait.description, HT.BR()) - #heading2.append(HT.Strong('Author: '), self.Trait.authors, HT.BR()) - else: - pass - else: - heading2.append(HT.Strong("Trait Name: "), fd.identification) - - if specialStrains: - mdpform = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), name='MDP_Form',submit=HT.Input(type='hidden')) - mdphddn = {'FormID':'dataEditing', 'submitID':'basicStatistics','RISet':fd.RISet, "allstrainlist":string.join(fd.allstrainlist, " "), "ptype":self.plotType, 'identification':fd.identification, "incparentsf1":1} - if self.fullname: mdphddn['fullname'] = self.fullname - webqtlUtil.exportData(mdphddn, fd.allTraitData) - for key in mdphddn.keys(): - mdpform.append(HT.Input(name=key, value=mdphddn[key], type='hidden')) - btn0 = HT.Input(type='button' ,name='',value='All Cases',onClick="this.form.ptype.value=0;submit();", Class="button") - btn1 = HT.Input(type='button' ,name='',value='%s Only' % fd.RISet,onClick="this.form.ptype.value=1;submit();", Class="button") - btn2 = HT.Input(type='button' ,name='',value='MDP Only', onClick="this.form.ptype.value=2;submit();", Class="button") - mdpform.append(btn0) - mdpform.append(btn1) - mdpform.append(btn2) - heading2.append(HT.P(), mdpform) - - return HT.Span(heading2) - - def calSD(self,var): - try: - return sqrt(abs(var)) - except: - return None - - - def cmpValue(self,A,B): - try: - if A[1] < B[1]: - return -1 - elif A[1] == B[1]: - return 0 - else: - return 1 - except: - return 0 - - - - + plotMinInformative = 4 + + def __init__(self, fd): + + templatePage.__init__(self, fd) + + if not fd.genotype: + fd.readGenotype() + strainlist2 = fd.strainlist + + if fd.allstrainlist: + strainlist2 = fd.allstrainlist + + fd.readData(strainlist2) + + specialStrains = [] + setStrains = [] + for item in strainlist2: + if item not in fd.strainlist and item.find('F1') < 0: + specialStrains.append(item) + else: + setStrains.append(item) + specialStrains.sort() + #So called MDP Panel + if specialStrains: + specialStrains = fd.f1list+fd.parlist+specialStrains + + self.plotType = fd.formdata.getvalue('ptype', '0') + plotStrains = strainlist2 + if specialStrains: + if self.plotType == '1': + plotStrains = setStrains + if self.plotType == '2': + plotStrains = specialStrains + + self.dict['title'] = 'Basic Statistics' + if not self.openMysql(): + return + + self.showstrains = 1 + self.identification = "unnamed trait" + + self.fullname = fd.formdata.getvalue('fullname', '') + if self.fullname: + self.Trait = webqtlTrait(fullname=self.fullname, cursor=self.cursor) + self.Trait.retrieveInfo() + else: + self.Trait = None + + if fd.identification: + self.identification = fd.identification + self.dict['title'] = self.identification + ' / '+self.dict['title'] + TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') + + ##should not display Variance, but cannot convert Variance to SE + #print plotStrains, fd.allTraitData.keys() + if len(fd.allTraitData) > 0: + vals=[] + InformData = [] + for _strain in plotStrains: + if fd.allTraitData.has_key(_strain): + _val, _var = fd.allTraitData[_strain].val, fd.allTraitData[_strain].var + if _val != None: + vals.append([_strain, _val, _var]) + InformData.append(_val) + + if len(vals) >= self.plotMinInformative: + supertable2 = HT.TableLite(border=0, cellspacing=0, cellpadding=5,width="800") + + staIntro1 = HT.Paragraph("The table and plots below list the basic statistical analysis result of trait",HT.Strong(" %s" % self.identification)) + + ##### + #anova + ##### + traitmean, traitmedian, traitvar, traitstdev, traitsem, N = reaper.anova(InformData) + TDStatis = HT.TD(width="360", valign="top") + tbl2 = HT.TableLite(cellpadding=5, cellspacing=0, Class="collap") + dataXZ = vals[:] + dataXZ.sort(self.cmpValue) + tbl2.append(HT.TR(HT.TD("Statistic",align="center", Class="fs14 fwb ffl b1 cw cbrb", width = 200), + HT.TD("Value", align="center", Class="fs14 fwb ffl b1 cw cbrb", width = 140))) + tbl2.append(HT.TR(HT.TD("N of Cases",align="center", Class="fs13 b1 cbw c222"), + HT.TD(N,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("Mean",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitmean,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("Median",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitmedian,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + #tbl2.append(HT.TR(HT.TD("Variance",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + # HT.TD("%2.3f" % traitvar,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("SEM",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitsem,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("SD",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitstdev,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("Minimum",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%s" % dataXZ[0][1],nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("Maximum",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%s" % dataXZ[-1][1],nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + if self.Trait and self.Trait.db.type == 'ProbeSet': + #IRQuest = HT.Href(text="Interquartile Range", url=webqtlConfig.glossaryfile +"#Interquartile",target="_blank", Class="fs14") + #IRQuest.append(HT.BR()) + #IRQuest.append(" (fold difference)") + tbl2.append(HT.TR(HT.TD("Range (log2)",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % (dataXZ[-1][1]-dataXZ[0][1]),nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD(HT.Span("Range (fold)"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.2f" % pow(2.0,(dataXZ[-1][1]-dataXZ[0][1])), nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD(HT.Span("Quartile Range",HT.BR()," (fold difference)"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.2f" % pow(2.0,(dataXZ[int((N-1)*3.0/4.0)][1]-dataXZ[int((N-1)/4.0)][1])), nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + + # (Lei Yan) + # 2008/12/19 + self.Trait.retrieveData() + #XZ, 04/01/2009: don't try to get H2 value for probe. + if self.Trait.cellid: + pass + else: + self.cursor.execute("SELECT DataId, h2 from ProbeSetXRef WHERE DataId = %d" % self.Trait.mysqlid) + dataid, heritability = self.cursor.fetchone() + if heritability: + tbl2.append(HT.TR(HT.TD(HT.Span("Heritability"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"),HT.TD("%s" % heritability, nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + else: + tbl2.append(HT.TR(HT.TD(HT.Span("Heritability"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"),HT.TD("NaN", nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + + # Lei Yan + # 2008/12/19 + + TDStatis.append(tbl2) + + plotHeight = 220 + plotWidth = 120 + xLeftOffset = 60 + xRightOffset = 25 + yTopOffset = 20 + yBottomOffset = 53 + + canvasHeight = plotHeight + yTopOffset + yBottomOffset + canvasWidth = plotWidth + xLeftOffset + xRightOffset + canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight)) + XXX = [('', InformData[:])] + + Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel= "Trait") + filename= webqtlUtil.genRandStr("Box_") + canvas.save(webqtlConfig.IMGDIR+filename, format='gif') + img=HT.Image('/image/'+filename+'.gif',border=0) + + #supertable2.append(HT.TR(HT.TD(staIntro1, colspan=3 ))) + tb = HT.TableLite(border=0, cellspacing=0, cellpadding=0) + tb.append(HT.TR(HT.TD(img, align="left", style="border: 1px solid #999999; padding:0px;"))) + supertable2.append(HT.TR(TDStatis, HT.TD(tb))) + + dataXZ = vals[:] + tvals = [] + tnames = [] + tvars = [] + for i in range(len(dataXZ)): + tvals.append(dataXZ[i][1]) + tnames.append(webqtlUtil.genShortStrainName(fd, dataXZ[i][0])) + tvars.append(dataXZ[i][2]) + nnStrain = len(tnames) + + sLabel = 1 + + ###determine bar width and space width + if nnStrain < 20: + sw = 4 + elif nnStrain < 40: + sw = 3 + else: + sw = 2 + + ### 700 is the default plot width minus Xoffsets for 40 strains + defaultWidth = 650 + if nnStrain > 40: + defaultWidth += (nnStrain-40)*10 + defaultOffset = 100 + bw = int(0.5+(defaultWidth - (nnStrain-1.0)*sw)/nnStrain) + if bw < 10: + bw = 10 + + plotWidth = (nnStrain-1)*sw + nnStrain*bw + defaultOffset + plotHeight = 500 + #print [plotWidth, plotHeight, bw, sw, nnStrain] + c = pid.PILCanvas(size=(plotWidth,plotHeight)) + Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title='%s by Case (sorted by name)' % self.identification, sLabel = sLabel, barSpace = sw) + + filename= webqtlUtil.genRandStr("Bar_") + c.save(webqtlConfig.IMGDIR+filename, format='gif') + img0=HT.Image('/image/'+filename+'.gif',border=0) + + dataXZ = vals[:] + dataXZ.sort(self.cmpValue) + tvals = [] + tnames = [] + tvars = [] + for i in range(len(dataXZ)): + tvals.append(dataXZ[i][1]) + tnames.append(webqtlUtil.genShortStrainName(fd, dataXZ[i][0])) + tvars.append(dataXZ[i][2]) + + c = pid.PILCanvas(size=(plotWidth,plotHeight)) + Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title='%s by Case (ranked)' % self.identification, sLabel = sLabel, barSpace = sw) + + filename= webqtlUtil.genRandStr("Bar_") + c.save(webqtlConfig.IMGDIR+filename, format='gif') + img1=HT.Image('/image/'+filename+'.gif',border=0) + + # Lei Yan + # 05/18/2009 + # report + + title = HT.Paragraph('REPORT on the variation of Shh (or PCA Composite Trait XXXX) (sonic hedgehog) in the (insert Data set name) of (insert Species informal name, e.g., Mouse, Rat, Human, Barley, Arabidopsis)', Class="title") + header = HT.Paragraph('''This report was generated by GeneNetwork on May 11, 2009, at 11.20 AM using the Basic Statistics module (v 1.0) and data from the Hippocampus Consortium M430v2 (Jun06) PDNN data set. For more details and updates on this data set please link to URL:get Basic Statistics''') + hr = HT.HR() + p1 = HT.Paragraph('''Trait values for Shh were taken from the (insert Database name, Hippocampus Consortium M430v2 (Jun06) PDNN). GeneNetwork contains data for NN (e.g., 99) cases. In general, data are averages for each case. A summary of mean, median, and the range of these data are provided in Table 1 and in the box plot (Figure 1). Data for individual cases are provided in Figure 2A and 2B, often with error bars (SEM). ''') + p2 = HT.Paragraph('''Trait values for Shh range 5.1-fold: from a low of 8.2 (please round value) in 129S1/SvImJ to a high of 10.6 (please round value) in BXD9. The interquartile range (the difference between values closest to the 25% and 75% levels) is a more modest 1.8-fold. The mean value is XX. ''') + t1 = HT.Paragraph('''Table 1. Summary of Shh data from the Hippocampus Consortium M430v2 (june06) PDNN data set''') + f1 = HT.Paragraph('''Figure 1. ''') + f1.append(HT.Href(text="Box plot", url="http://davidmlane.com/hyperstat/A37797.html", target="_blank", Class="fs14")) + f1.append(HT.Text(''' of Shh data from the Hippocampus Consortium M430v2 (june06) PDNN data set''')) + f2A = HT.Paragraph('''Figure 2A: Bar chart of Shh data ordered by case from the Hippocampus Consortium M430v2 (june06) PDNN data set''') + f2B = HT.Paragraph('''Figure 2B: Bar chart of Shh values ordered by from the Hippocampus Consortium M430v2 (june06) PDNN data set''') + TD_LR.append(HT.Blockquote(title, HT.P(), header, hr, p1, HT.P(), p2, HT.P(), supertable2, t1, f1, HT.P(), img0, f2A, HT.P(), img1, f2B)) + self.dict['body'] = str(TD_LR) + else: + heading = "Basic Statistics" + detail = ['Fewer than %d case data were entered for %s data set. No statitical analysis has been attempted.' % (self.plotMinInformative, fd.RISet)] + self.error(heading=heading,detail=detail) + return + else: + heading = "Basic Statistics" + detail = ['Empty data set, please check your data.'] + self.error(heading=heading,detail=detail) + return + + def traitInfo(self, fd, specialStrains = None): + species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) + heading2 = HT.Paragraph(HT.Strong('Population: '), "%s %s" % (species.title(), fd.RISet) , HT.BR()) + if self.Trait: + trait_url = HT.Href(text=self.Trait.name, url = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + \ + "?FormID=showDatabase&incparentsf1=1&database=%s&ProbeSetID=%s" % (self.Trait.db.name, self.Trait.name), \ + target='_blank', Class="fs13 fwn") + heading2.append(HT.Strong("Database: "), + HT.Href(text=self.Trait.db.fullname, url = webqtlConfig.INFOPAGEHREF % self.Trait.db.name , + target='_blank',Class="fs13 fwn"),HT.BR()) + if self.Trait.db.type == 'ProbeSet': + heading2.append(HT.Strong('Trait ID: '), trait_url, HT.BR(), + HT.Strong("Gene Symbol: "), HT.Italic('%s' % self.Trait.symbol,id="green"),HT.BR()) + if self.Trait.chr and self.Trait.mb: + heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (self.Trait.chr, self.Trait.mb)) + elif self.Trait.db.type == 'Geno': + heading2.append(HT.Strong('Locus : '), trait_url, HT.BR()) + #heading2.append(HT.Strong("Gene Symbol: "), HT.Italic('%s' % self.Trait.Symbol,id="green"),HT.BR()) + if self.Trait.chr and self.Trait.mb: + heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (self.Trait.chr, self.Trait.mb)) + elif self.Trait.db.type == 'Publish': + heading2.append(HT.Strong('Record ID: '), trait_url, HT.BR()) + heading2.append(HT.Strong('Phenotype: '), self.Trait.phenotype, HT.BR()) + heading2.append(HT.Strong('Author: '), self.Trait.authors, HT.BR()) + elif self.Trait.db.type == 'Temp': + heading2.append(HT.Strong('Description: '), self.Trait.description, HT.BR()) + #heading2.append(HT.Strong('Author: '), self.Trait.authors, HT.BR()) + else: + pass + else: + heading2.append(HT.Strong("Trait Name: "), fd.identification) + + if specialStrains: + mdpform = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), name='MDP_Form',submit=HT.Input(type='hidden')) + mdphddn = {'FormID':'dataEditing', 'submitID':'basicStatistics','RISet':fd.RISet, "allstrainlist":string.join(fd.allstrainlist, " "), "ptype":self.plotType, 'identification':fd.identification, "incparentsf1":1} + if self.fullname: mdphddn['fullname'] = self.fullname + webqtlUtil.exportData(mdphddn, fd.allTraitData) + for key in mdphddn.keys(): + mdpform.append(HT.Input(name=key, value=mdphddn[key], type='hidden')) + btn0 = HT.Input(type='button' ,name='',value='All Cases',onClick="this.form.ptype.value=0;submit();", Class="button") + btn1 = HT.Input(type='button' ,name='',value='%s Only' % fd.RISet,onClick="this.form.ptype.value=1;submit();", Class="button") + btn2 = HT.Input(type='button' ,name='',value='MDP Only', onClick="this.form.ptype.value=2;submit();", Class="button") + mdpform.append(btn0) + mdpform.append(btn1) + mdpform.append(btn2) + heading2.append(HT.P(), mdpform) + + return HT.Span(heading2) + + def calSD(self,var): + try: + return sqrt(abs(var)) + except: + return None + + + def cmpValue(self,A,B): + try: + if A[1] < B[1]: + return -1 + elif A[1] == B[1]: + return 0 + else: + return 1 + except: + return 0 diff --git a/wqflask/basicStatistics/updatedBasicStatisticsPage.py b/wqflask/basicStatistics/updatedBasicStatisticsPage.py index ab7ed07d..3f30619d 100755 --- a/wqflask/basicStatistics/updatedBasicStatisticsPage.py +++ b/wqflask/basicStatistics/updatedBasicStatisticsPage.py @@ -6,145 +6,145 @@ import BasicStatisticsFunctions #Window generated from the Trait Data and Analysis page (DataEditingPage.py) with updated stats figures; takes the page's values that can bed edited by the user class updatedBasicStatisticsPage(templatePage): - - plotMinInformative = 4 - - def __init__(self, fd): - - templatePage.__init__(self, fd) - - if not fd.genotype: - fd.readGenotype() - this_strainlist = fd.strainlist - - if fd.allstrainlist: - this_strainlist = fd.allstrainlist - - fd.readData(this_strainlist) - - specialStrains = [] #This appears to be the "other/non-RISet strainlist" without parents/f1 strains; not sure what to name it - setStrains = [] - for item in this_strainlist: - if item not in fd.strainlist and item.find('F1') < 0: - specialStrains.append(item) - else: - continue - - specialStrains.sort() - if specialStrains: - specialStrains = fd.f1list+fd.parlist+specialStrains - - self.dict['title'] = 'Basic Statistics' - TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa") - - stats_row = HT.TR() - stats_cell = HT.TD() - stats_script = HT.Script(language="Javascript") - - #Get strain names, values, and variances - strain_names = fd.formdata.getvalue('strainNames').split(',') - strain_vals = fd.formdata.getvalue('strainVals').split(',') - strain_vars = fd.formdata.getvalue('strainVars').split(',') - - vals = [] - if (len(strain_names) > 0): - if (len(strain_names) > 3): - #Need to create "vals" object - for i in range(len(strain_names)): - try: - this_strain_val = float(strain_vals[i]) - except: - continue - try: - this_strain_var = float(strain_vars[i]) - except: - this_strain_var = None - - thisValFull = [strain_names[i], this_strain_val, this_strain_var] - vals.append(thisValFull) - - stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-2", Class="stats_tab"), - HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"), - HT.Href(text="Box Plot", url="#statstabs-5", Class="stats_tab")] - stats_tabs = HT.List(stats_tab_list) - - stats_container = HT.Div(id="stats_tabs", Class="ui-tabs") - stats_container.append(stats_tabs) - - stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" #Javascript enabling tabs - - table_div = HT.Div(id="statstabs-1", style="height:320px;width:740px;overflow:scroll;") - table_container = HT.Paragraph() - - statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - this_trait_type = fd.formdata.getvalue('trait_type', None) - this_cellid = fd.formdata.getvalue('cellid', None) - statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=this_trait_type, cellid=this_cellid) - statsTable.append(HT.TR(HT.TD(statsTableCell))) - - table_container.append(statsTable) - table_div.append(table_container) - stats_container.append(table_div) - - normalplot_div = HT.Div(id="statstabs-2", style="height:540px;width:740px;overflow:scroll;") - normalplot_container = HT.Paragraph() - normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - plotTitle = fd.formdata.getvalue("normalPlotTitle","") - normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains) - normalplot.append(HT.TR(HT.TD(normalplot_img))) - normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \ - normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(), - "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", - target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary")))) - normalplot_container.append(normalplot) - normalplot_div.append(normalplot_container) - stats_container.append(normalplot_div) - - barName_div = HT.Div(id="statstabs-3", style="height:540px;width:740px;overflow:scroll;") - barName_container = HT.Paragraph() - barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name") - barName.append(HT.TR(HT.TD(barName_img))) - barName_container.append(barName) - barName_div.append(barName_container) - stats_container.append(barName_div) - - barRank_div = HT.Div(id="statstabs-4", style="height:540px;width:740px;overflow:scroll;") - barRank_container = HT.Paragraph() - barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank") - barRank.append(HT.TR(HT.TD(barRank_img))) - barRank_container.append(barRank) - barRank_div.append(barRank_container) - stats_container.append(barRank_div) - - boxplot_div = HT.Div(id="statstabs-5", style="height:540px;width:740px;overflow:scroll;") - boxplot_container = HT.Paragraph() - boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals) - boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left"))) - boxplot_container.append(boxplot) - boxplot_div.append(boxplot_container) - stats_container.append(boxplot_div) - - stats_cell.append(stats_container) - stats_script.append(stats_script_text) - - submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - stats_row.append(stats_cell) - - submitTable.append(stats_row) - submitTable.append(stats_script) - - TD_LR.append(submitTable) - self.dict['body'] = str(TD_LR) - else: - heading = "Basic Statistics" - detail = ['Fewer than %d case data were entered for %s data set. No statitical analysis has been attempted.' % (self.plotMinInformative, fd.RISet)] - self.error(heading=heading,detail=detail) - return - else: - heading = "Basic Statistics" - detail = ['Empty data set, please check your data.'] - self.error(heading=heading,detail=detail) - return \ No newline at end of file + + plotMinInformative = 4 + + def __init__(self, fd): + + templatePage.__init__(self, fd) + + if not fd.genotype: + fd.readGenotype() + this_strainlist = fd.strainlist + + if fd.allstrainlist: + this_strainlist = fd.allstrainlist + + fd.readData(this_strainlist) + + specialStrains = [] #This appears to be the "other/non-RISet strainlist" without parents/f1 strains; not sure what to name it + setStrains = [] + for item in this_strainlist: + if item not in fd.strainlist and item.find('F1') < 0: + specialStrains.append(item) + else: + continue + + specialStrains.sort() + if specialStrains: + specialStrains = fd.f1list+fd.parlist+specialStrains + + self.dict['title'] = 'Basic Statistics' + TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa") + + stats_row = HT.TR() + stats_cell = HT.TD() + stats_script = HT.Script(language="Javascript") + + #Get strain names, values, and variances + strain_names = fd.formdata.getvalue('strainNames').split(',') + strain_vals = fd.formdata.getvalue('strainVals').split(',') + strain_vars = fd.formdata.getvalue('strainVars').split(',') + + vals = [] + if (len(strain_names) > 0): + if (len(strain_names) > 3): + #Need to create "vals" object + for i in range(len(strain_names)): + try: + this_strain_val = float(strain_vals[i]) + except: + continue + try: + this_strain_var = float(strain_vars[i]) + except: + this_strain_var = None + + thisValFull = [strain_names[i], this_strain_val, this_strain_var] + vals.append(thisValFull) + + stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-2", Class="stats_tab"), + HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"), + HT.Href(text="Box Plot", url="#statstabs-5", Class="stats_tab")] + stats_tabs = HT.List(stats_tab_list) + + stats_container = HT.Div(id="stats_tabs", Class="ui-tabs") + stats_container.append(stats_tabs) + + stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" #Javascript enabling tabs + + table_div = HT.Div(id="statstabs-1", style="height:320px;width:740px;overflow:scroll;") + table_container = HT.Paragraph() + + statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + this_trait_type = fd.formdata.getvalue('trait_type', None) + this_cellid = fd.formdata.getvalue('cellid', None) + statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=this_trait_type, cellid=this_cellid) + statsTable.append(HT.TR(HT.TD(statsTableCell))) + + table_container.append(statsTable) + table_div.append(table_container) + stats_container.append(table_div) + + normalplot_div = HT.Div(id="statstabs-2", style="height:540px;width:740px;overflow:scroll;") + normalplot_container = HT.Paragraph() + normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + plotTitle = fd.formdata.getvalue("normalPlotTitle","") + normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains) + normalplot.append(HT.TR(HT.TD(normalplot_img))) + normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \ + normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(), + "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", + target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary")))) + normalplot_container.append(normalplot) + normalplot_div.append(normalplot_container) + stats_container.append(normalplot_div) + + barName_div = HT.Div(id="statstabs-3", style="height:540px;width:740px;overflow:scroll;") + barName_container = HT.Paragraph() + barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name") + barName.append(HT.TR(HT.TD(barName_img))) + barName_container.append(barName) + barName_div.append(barName_container) + stats_container.append(barName_div) + + barRank_div = HT.Div(id="statstabs-4", style="height:540px;width:740px;overflow:scroll;") + barRank_container = HT.Paragraph() + barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank") + barRank.append(HT.TR(HT.TD(barRank_img))) + barRank_container.append(barRank) + barRank_div.append(barRank_container) + stats_container.append(barRank_div) + + boxplot_div = HT.Div(id="statstabs-5", style="height:540px;width:740px;overflow:scroll;") + boxplot_container = HT.Paragraph() + boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals) + boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left"))) + boxplot_container.append(boxplot) + boxplot_div.append(boxplot_container) + stats_container.append(boxplot_div) + + stats_cell.append(stats_container) + stats_script.append(stats_script_text) + + submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + stats_row.append(stats_cell) + + submitTable.append(stats_row) + submitTable.append(stats_script) + + TD_LR.append(submitTable) + self.dict['body'] = str(TD_LR) + else: + heading = "Basic Statistics" + detail = ['Fewer than %d case data were entered for %s data set. No statitical analysis has been attempted.' % (self.plotMinInformative, fd.RISet)] + self.error(heading=heading,detail=detail) + return + else: + heading = "Basic Statistics" + detail = ['Empty data set, please check your data.'] + self.error(heading=heading,detail=detail) + return diff --git a/wqflask/dbFunction/webqtlDatabaseFunction.py b/wqflask/dbFunction/webqtlDatabaseFunction.py index 772e0526..7e33da3f 100755 --- a/wqflask/dbFunction/webqtlDatabaseFunction.py +++ b/wqflask/dbFunction/webqtlDatabaseFunction.py @@ -26,7 +26,7 @@ #webqtlDatabaseFunction.py # -#This file consists of various database related functions; the names are generally self-explanatory. +#This file consists of various database related functions; the names are generally self-explanatory. import MySQLdb import string @@ -49,63 +49,63 @@ def getCursor(): ########################################################################### #input: cursor, groupName (string) #output: mappingMethodId (int) info, value will be Null or else -#function: retrieve mappingMethodId info from InbredSet table -########################################################################### +#function: retrieve mappingMethodId info from InbredSet table +########################################################################### def getMappingMethod(cursor=None, groupName=None): - cursor.execute("select MappingMethodId from InbredSet where Name= '%s'" % groupName) - mappingMethodId = cursor.fetchone()[0] - return mappingMethodId + cursor.execute("select MappingMethodId from InbredSet where Name= '%s'" % groupName) + mappingMethodId = cursor.fetchone()[0] + return mappingMethodId ########################################################################### #input: cursor, inbredSetId (int), strainId (int) -#output: isMappingId (bull) info, value will be 0,1,2 or else, 0 or Null means -# "can not do mapping", >0 means "can do mapping", >1 means "there exsists +#output: isMappingId (bull) info, value will be 0,1,2 or else, 0 or Null means +# "can not do mapping", >0 means "can do mapping", >1 means "there exsists # redundant data, user needs to choose one to do mapping function" -#function: retrieve isMappingId info from StrainXRef table -########################################################################### - -def isMapping(cursor=None, inbredSetId=None, strainId=None): - cursor.execute("select IsMapping from StrainXRef where InbredSetId='%d' and StrainId = '%d'" %(inbredSetId, strainId)) - isMappingId = cursor.fetchone()[0] - return isMappingId +#function: retrieve isMappingId info from StrainXRef table +########################################################################### + +def isMapping(cursor=None, inbredSetId=None, strainId=None): + cursor.execute("select IsMapping from StrainXRef where InbredSetId='%d' and StrainId = '%d'" %(inbredSetId, strainId)) + isMappingId = cursor.fetchone()[0] + return isMappingId ########################################################################### #input: cursor, groupName (string) #output: all species data info (array), value will be Null or else -#function: retrieve all species info from Species table -########################################################################### +#function: retrieve all species info from Species table +########################################################################### def getAllSpecies(cursor=None): - cursor.execute("select Id, Name, MenuName, FullName, TaxonomyId,OrderId from Species Order by OrderId") - allSpecies = cursor.fetchall() - return allSpecies + cursor.execute("select Id, Name, MenuName, FullName, TaxonomyId,OrderId from Species Order by OrderId") + allSpecies = cursor.fetchall() + return allSpecies ########################################################################### #input: cursor, RISet (string) #output: specie's name (string), value will be None or else -#function: retrieve specie's name info based on RISet -########################################################################### +#function: retrieve specie's name info based on RISet +########################################################################### def retrieveSpecies(cursor=None, RISet=None): - try: - cursor.execute("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % RISet) - return cursor.fetchone()[0] - except: - return None + try: + cursor.execute("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % RISet) + return cursor.fetchone()[0] + except: + return None ########################################################################### #input: cursor, RISet (string) #output: specie's Id (string), value will be None or else -#function: retrieve specie's Id info based on RISet -########################################################################### - +#function: retrieve specie's Id info based on RISet +########################################################################### + def retrieveSpeciesId(cursor=None, RISet=None): - try: - cursor.execute("select SpeciesId from InbredSet where Name = '%s'" % RISet) - return cursor.fetchone()[0] - except: - return None + try: + cursor.execute("select SpeciesId from InbredSet where Name = '%s'" % RISet) + return cursor.fetchone()[0] + except: + return None ########################################################################### # input: cursor @@ -118,24 +118,24 @@ def retrieveSpeciesId(cursor=None, RISet=None): ########################################################################### def getTissueDataSet(cursor=None): - tissProbeSetFreezeIdList=[] - nameList =[] - fullNameList = [] - - query = "select Id,Name,FullName from TissueProbeSetFreeze; " - try: - cursor.execute(query) - result = cursor.fetchall() - - for row in result: - tissProbeSetFreezeIdList.append(row[0]) - nameList.append(row[1]) - fullNameList.append(row[2]) - except: - return None - - return tissProbeSetFreezeIdList,nameList,fullNameList - + tissProbeSetFreezeIdList=[] + nameList =[] + fullNameList = [] + + query = "select Id,Name,FullName from TissueProbeSetFreeze; " + try: + cursor.execute(query) + result = cursor.fetchall() + + for row in result: + tissProbeSetFreezeIdList.append(row[0]) + nameList.append(row[1]) + fullNameList.append(row[2]) + except: + return None + + return tissProbeSetFreezeIdList,nameList,fullNameList + ########################################################################### # input: cursor,GeneSymbol (string), and TissueProbeSetFreezeId (string) # output: geneId (string), dataId (string) @@ -143,42 +143,42 @@ def getTissueDataSet(cursor=None): ########################################################################### def getGeneIdDataIdForTissueBySymbol(cursor=None, GeneSymbol=None, TissueProbeSetFreezeId= 0): - query ="select GeneId, DataId from TissueProbeSetXRef where Symbol = '%s' and TissueProbeSetFreezeId=%s order by Mean desc" %(GeneSymbol,TissueProbeSetFreezeId) - try: - cursor.execute(query) - result = cursor.fetchone() - geneId = result[0] - dataId = result[1] - except: - geneId = 0 - dataId = 0 - - return geneId,dataId + query ="select GeneId, DataId from TissueProbeSetXRef where Symbol = '%s' and TissueProbeSetFreezeId=%s order by Mean desc" %(GeneSymbol,TissueProbeSetFreezeId) + try: + cursor.execute(query) + result = cursor.fetchone() + geneId = result[0] + dataId = result[1] + except: + geneId = 0 + dataId = 0 + + return geneId,dataId ########################################################################### # input: cursor, TissueProbeSetFreezeId (int) # output: chipId (int) -# function: retrieve chipId from TissueProbeFreeze table +# function: retrieve chipId from TissueProbeFreeze table ########################################################################### def getChipIdByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None): - query = "select TissueProbeFreezeId from TissueProbeSetFreeze where Id =%s" % TissueProbeSetFreezeId - try: - cursor.execute(query) - result = cursor.fetchone() - TissueProbeFreezeId = result[0] - except: - TissueProbeFreezeId =0 - - query1 = "select ChipId from TissueProbeFreeze where Id =%s" % TissueProbeFreezeId - try: - cursor.execute(query1) - result1 = cursor.fetchone() - chipId = result1[0] - except: - chipId =0 - - return chipId + query = "select TissueProbeFreezeId from TissueProbeSetFreeze where Id =%s" % TissueProbeSetFreezeId + try: + cursor.execute(query) + result = cursor.fetchone() + TissueProbeFreezeId = result[0] + except: + TissueProbeFreezeId =0 + + query1 = "select ChipId from TissueProbeFreeze where Id =%s" % TissueProbeFreezeId + try: + cursor.execute(query1) + result1 = cursor.fetchone() + chipId = result1[0] + except: + chipId =0 + + return chipId ########################################################################### # input: cursor, TissueProbeSetFreezeId (int) @@ -186,80 +186,79 @@ def getChipIdByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None): # function: retrieve how many tissue used in the specific dataset based on TissueProbeSetFreezeId ########################################################################### def getTissueCountByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None): - query1 ="select DataId from TissueProbeSetXRef where TissueProbeSetFreezeId =%s limit 1" % TissueProbeSetFreezeId - try: - cursor.execute(query1) - result1 = cursor.fetchone() - DataId = result1[0] - - query2 =" select count(*) from TissueProbeSetData where Id=%s" % DataId - try: - cursor.execute(query2) - result2 = cursor.fetchone() - TissueCount = result2[0] - except: - TissueCount =0 - except: - TissueCount =0 - - return TissueCount - + query1 ="select DataId from TissueProbeSetXRef where TissueProbeSetFreezeId =%s limit 1" % TissueProbeSetFreezeId + try: + cursor.execute(query1) + result1 = cursor.fetchone() + DataId = result1[0] + + query2 =" select count(*) from TissueProbeSetData where Id=%s" % DataId + try: + cursor.execute(query2) + result2 = cursor.fetchone() + TissueCount = result2[0] + except: + TissueCount =0 + except: + TissueCount =0 + + return TissueCount + ########################################################################### # input: cursor, TissueProbeSetFreezeId (int) # output: DatasetName(string),DatasetFullName(string) # function: retrieve DatasetName, DatasetFullName based on TissueProbeSetFreezeId ########################################################################### def getDatasetNamesByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None): - query ="select Name, FullName from TissueProbeSetFreeze where Id=%s" % TissueProbeSetFreezeId - try: - cursor.execute(query) - result = cursor.fetchone() - DatasetName = result[0] - DatasetFullName =result[1] - except: - DatasetName =None - DatasetFullName =None - - return DatasetName, DatasetFullName - + query ="select Name, FullName from TissueProbeSetFreeze where Id=%s" % TissueProbeSetFreezeId + try: + cursor.execute(query) + result = cursor.fetchone() + DatasetName = result[0] + DatasetFullName =result[1] + except: + DatasetName =None + DatasetFullName =None + + return DatasetName, DatasetFullName + ########################################################################### # input: cursor, geneIdLst (list) # output: geneIdSymbolPair(dict),key is geneId, value is geneSymbol # function: retrieve GeneId, GeneSymbol based on geneId List -########################################################################### +########################################################################### def getGeneIdSymbolPairByGeneId(cursor=None, geneIdLst =None): - geneIdSymbolPair={} - for geneId in geneIdLst: - geneIdSymbolPair[geneId]=None - - query ="select GeneId,GeneSymbol from GeneList where GeneId in (%s)" % string.join(geneIdLst, ", ") - try: - cursor.execute(query) - results = cursor.fetchall() - for item in results: - geneId =item[0] - geneSymbol =item[1] - geneIdSymbolPair[geneId]=geneSymbol - except: - geneIdSymbolPair=None - - return geneIdSymbolPair - - + geneIdSymbolPair={} + for geneId in geneIdLst: + geneIdSymbolPair[geneId]=None + + query ="select GeneId,GeneSymbol from GeneList where GeneId in (%s)" % string.join(geneIdLst, ", ") + try: + cursor.execute(query) + results = cursor.fetchall() + for item in results: + geneId =item[0] + geneSymbol =item[1] + geneIdSymbolPair[geneId]=geneSymbol + except: + geneIdSymbolPair=None + + return geneIdSymbolPair + + def updateTissueProbesetXRefByProbesetId(cursor=None, probesetId=None): - query ="select Symbol,GeneId,Chr,Mb,description, Probe_Target_Description from ProbeSet where Id =%s"%probesetId - try: - cursor.execute(query) - result =cursor.fetchone() - - updateQuery =''' - Update TissueProbeSetXRef - Set Symbol='%s',GeneId='%s', Chr='%s', Mb='%s', description ='%s',Probe_Target_Description='%s' - where ProbesetId=%s - '''%(result[0],result[1],result[2],result[3],result[4],result[5],probesetId) - - cursor.execute(updateQuery) - - except: - return None - \ No newline at end of file + query ="select Symbol,GeneId,Chr,Mb,description, Probe_Target_Description from ProbeSet where Id =%s"%probesetId + try: + cursor.execute(query) + result =cursor.fetchone() + + updateQuery =''' + Update TissueProbeSetXRef + Set Symbol='%s',GeneId='%s', Chr='%s', Mb='%s', description ='%s',Probe_Target_Description='%s' + where ProbesetId=%s + '''%(result[0],result[1],result[2],result[3],result[4],result[5],probesetId) + + cursor.execute(updateQuery) + + except: + return None diff --git a/wqflask/utility/AJAX_table.py b/wqflask/utility/AJAX_table.py index 963a530e..083d1c0d 100755 --- a/wqflask/utility/AJAX_table.py +++ b/wqflask/utility/AJAX_table.py @@ -39,115 +39,115 @@ 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 = "The table is no longer available on this server" - - def __str__(self): - return self.value - - def write(self): - return str(self) + 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 = "The table is no longer available on this server" + + def __str__(self): + return self.value + + def write(self): + return str(self) diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index e00b8e9e..04fe85bf 100755 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -39,1245 +39,1245 @@ 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 + '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 + "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 + 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) + 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)=0.0: - return ans - else: - return 2.0-ans + 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 + 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] + #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] + 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] + 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] + d = [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00] - #Define break-points. + #Define break-points. - p_low = 0.02425 - p_high = 1 - p_low + p_low = 0.02425 + p_high = 1 - p_low - #Rational approximation for lower region. + #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) + 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. + #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) + 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. + #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) + 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 + 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 + 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 + 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] + 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]) + 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 + 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) + 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 + 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) + 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 + 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 + '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 + '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)] + 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] + 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 + 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))) + return 1.0 / (1.0 + exp(-10*(x-0.6))) def redfunc(x): - return 1.0 / (1.0 + exp(10*(x-0.5))) + 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) + 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 + 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 + 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 + 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/wqflask/utility/TDCell.py b/wqflask/utility/TDCell.py index 76b9c5db..8de8e050 100755 --- a/wqflask/utility/TDCell.py +++ b/wqflask/utility/TDCell.py @@ -30,13 +30,12 @@ # ########################################################## - + 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 + 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/wqflask/utility/THCell.py b/wqflask/utility/THCell.py index a96b9e49..dde221b5 100755 --- a/wqflask/utility/THCell.py +++ b/wqflask/utility/THCell.py @@ -32,13 +32,11 @@ 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 - + 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/wqflask/utility/svg.py b/wqflask/utility/svg.py index e49a6c3c..512bc9e6 100755 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -74,7 +74,7 @@ by using easy to use classes and methods usualy you start by creating a 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;) @@ -112,7 +112,7 @@ 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. @@ -167,7 +167,7 @@ def _xypointlist(a): def _viewboxlist(a): """formats a tuple""" s='' - for e in a: + for e in a: s+=str(e)+' ' return s @@ -178,7 +178,7 @@ def _pointlist(a): 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. + #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: @@ -242,10 +242,10 @@ class pathdata: 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. @@ -296,7 +296,7 @@ class SVGelement: if self.cdata: f.write('\n'+'\t'*(level+1)+'\n') if self.text: if type(self.text)==type(''): #If the text is only text @@ -305,13 +305,13 @@ class SVGelement: f.write(str(self.text)) if self.elements: f.write('\t'*level+'\n') - elif self.text: + elif self.text: f.write('\n') elif self.cdata: f.write('\t'*level+'\n') else: f.write('/>\n') - + class tspan(SVGelement): """ts=tspan(text='',**args) @@ -330,12 +330,12 @@ class tspan(SVGelement): def __repr__(self): s="None: self.attributes['stroke-width']=stroke_width - + class ellipse(SVGelement): """e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args) @@ -440,8 +440,8 @@ class ellipse(SVGelement): 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) @@ -464,7 +464,7 @@ class circle(SVGelement): 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. """ @@ -473,7 +473,7 @@ class point(circle): 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): @@ -490,10 +490,10 @@ class line(SVGelement): 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): @@ -507,7 +507,7 @@ class polyline(SVGelement): 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): @@ -534,11 +534,11 @@ class path(SVGelement): 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): @@ -560,7 +560,7 @@ class text(SVGelement): class textpath(SVGelement): """tp=textpath(text,link,**args) - a textpath places a text on a path which is referenced by a link. + 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) @@ -589,7 +589,7 @@ class pattern(SVGelement): 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 """ @@ -600,7 +600,7 @@ class title(SVGelement): 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. """ @@ -648,7 +648,7 @@ class radialgradient(SVGelement): self.attributes['fy']=fy if id<>None: self.attributes['id']=id - + class stop(SVGelement): """st=stop(offset,stop_color,**args) @@ -658,7 +658,7 @@ class stop(SVGelement): 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) @@ -666,8 +666,8 @@ class style(SVGelement): """ 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) @@ -686,7 +686,7 @@ class image(SVGelement): self.attributes['x']=x if y<>None: self.attributes['y']=y - + class cursor(SVGelement): """c=cursor(url,**args) @@ -695,10 +695,10 @@ class cursor(SVGelement): 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. """ @@ -716,10 +716,10 @@ class marker(SVGelement): 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) """ @@ -736,14 +736,14 @@ class symbol(SVGelement): 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) @@ -762,10 +762,10 @@ class switch(SVGelement): 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): @@ -779,8 +779,8 @@ class use(SVGelement): self.attributes['width']=width if height<>None: self.attributes['height']=height - - + + class link(SVGelement): """a=link(url,**args) @@ -789,7 +789,7 @@ class link(SVGelement): """ def __init__(self,link='',**args): SVGelement.__init__(self,'a',{'xlink:href':link},**args) - + class view(SVGelement): """v=view(id,**args) @@ -807,11 +807,11 @@ class script(SVGelement): """ 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. + animates an attribute. """ def __init__(self,attribute,fr=None,to=None,dur=None,**args): SVGelement.__init__(self,'animate',{'attributeName':attribute},**args) @@ -821,7 +821,7 @@ class animate(SVGelement): self.attributes['to']=to if dur<>None: self.attributes['dur']=dur - + class animateMotion(SVGelement): """an=animateMotion(pathdata,dur,**args) @@ -836,7 +836,7 @@ class animateMotion(SVGelement): 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): @@ -864,10 +864,10 @@ class animateColor(SVGelement): if to<>None: self.attributes['to']=to if dur<>None: - self.attributes['dur']=dur + 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): @@ -878,10 +878,10 @@ class set(SVGelement): 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) @@ -903,7 +903,7 @@ class svg(SVGelement): if height<>None: self.attributes['height']=height self.namespace="http://www.w3.org/2000/svg" - + class drawing: """d=drawing() @@ -921,17 +921,17 @@ class drawing: def setSVG(self,svg): self.svg=svg #Voeg een element toe aan de grafiek toe. - if use_dom_implementation==0: + if use_dom_implementation==0: def toXml(self, filename='',compress=False): import cStringIO xml=cStringIO.StringIO() xml.write("\n") xml.write("\n" % (item, self.entity[item])) - xml.write("]") + xml.write(" [\n") + for item in self.entity.keys(): + xml.write("\n" % (item, self.entity[item])) + xml.write("]") xml.write(">\n") self.svg.toXml(0,xml) if not filename: @@ -964,7 +964,7 @@ class drawing: 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. @@ -1034,12 +1034,12 @@ class drawing: 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') @@ -1064,6 +1064,5 @@ if __name__=='__main__': c=circle(i,j,1,'red','black',.5) s.addElement(c) d.setSVG(s) - - print d.toXml() + print d.toXml() diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index 6af7f846..6409e781 100755 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -90,741 +90,741 @@ PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle", ######################################### 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 - + 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 - + 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 + #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 + "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]))] + '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]))] + '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 + 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() + import sha + return sha.new(str(time.time())).hexdigest() def cvt2Dict(x): - tmp = {} - for key in x.keys(): - tmp[key] = x[key] - return tmp + 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() - + "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 - + '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 - + '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 + '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 + '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' + '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 + 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 "" + '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 - + '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'\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 + 'Remove the description text from the input file if theres any' + i=0 + while 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[1]: - return offset + 2 - else: - return offset +1 - elif n == 1: - if a lst[1]: + return offset + 2 + else: + return offset +1 + elif n == 1: + if a B.LRS: - return 1 - elif A.LRS == B.LRS: - return 0 - else: - return -1 - except: - return 0 - - + 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 + 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 + 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 + 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) + """ + 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) - - + """ + 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) + """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) + 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) + """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 + """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 + 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 + 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 + 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 + 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 + 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 - - + 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 - + 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 + 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) + 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): @@ -840,9 +840,9 @@ def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users) class VisualizeException(Exception): def __init__(self, message): - self.message = message + self.message = message def __str__(self): - return self.message + return self.message # safeConvert : (string -> A) -> A -> A # to convert a string to type A, using the supplied default value @@ -852,12 +852,12 @@ def safeConvert(f, value, default): 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): @@ -878,7 +878,7 @@ def yesNoToInt(value): if value == "yes": return 1 elif value == "no": - return 0 + return 0 else: return None @@ -890,79 +890,79 @@ def intToYesNo(value): elif value == 0: return "no" else: - return None - + return None + def formatField(name): - name = name.replace("_", " ") - name = name.title() - #name = name.replace("Mb Mm6", "Mb"); - return name.replace("Id", "ID") + 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 + 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 = [] @@ -974,4 +974,3 @@ def natsort_key(string): except: r.append(c) return r - diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index b50428fc..6d709012 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -18,1908 +18,1908 @@ from basicStatistics import BasicStatisticsFunctions ######################################### class DataEditingPage(templatePage): - def __init__(self, fd, thisTrait=None): - - templatePage.__init__(self, fd) - - self.dict['title'] = 'Data Editing' - TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa") - - if not self.openMysql(): - return - if not fd.genotype: - fd.readData(incf1=1) - - ############################# - # determine data editing page format - ############################# - varianceDataPage = 0 - if fd.formID == 'varianceChoice': - varianceDataPage = 1 - - if varianceDataPage: - fmID='dataEditing' - nCols = 6 - else: - if fd.enablevariance: - fmID='pre_dataEditing' - nCols = 4 - else: - fmID='dataEditing' - nCols = 4 - - ############################# - ## titles, etc. - ############################# - - #titleTop = HT.Div() - # - #title1 = HT.Paragraph("  Details and Links", style="border-radius: 5px;", Id="title1", Class="sectionheader") - #title1Body = HT.Paragraph(Id="sectionbody1") - # - #if fd.enablevariance and not varianceDataPage: - # title2 = HT.Paragraph("  Submit Variance", style="border-radius: 5px;", Id="title2", Class="sectionheader") - #else: - # title2 = HT.Paragraph("  Basic Statistics", style="border-radius: 5px;", Id="title2", Class="sectionheader") - #title2Body = HT.Paragraph(Id="sectionbody2") - # - #title3 = HT.Paragraph("  Calculate Correlations", style="border-radius: 5px;", Id="title3", Class="sectionheader") - #title3Body = HT.Paragraph(Id="sectionbody3") - # - #title4 = HT.Paragraph("  Mapping Tools", style="border-radius: 5px;", Id="title4", Class="sectionheader") - #title4Body = HT.Paragraph(Id="sectionbody4") - # - #title5 = HT.Paragraph("  Review and Edit Data", style="border-radius: 5px;", Id="title5", Class="sectionheader") - #title5Body = HT.Paragraph(Id="sectionbody5") - - ############################# - ## Hidden field - ############################# - - # Some fields, like method, are defaulted to None; otherwise in IE the field can't be changed using jquery - hddn = { - 'FormID':fmID, - 'RISet':fd.RISet, - 'submitID':'', - 'scale':'physic', - 'additiveCheck':'ON', - 'showSNP':'ON', - 'showGenes':'ON', - 'method':None, - 'parentsf14regression':'OFF', - 'stats_method':'1', - 'chromosomes':'-1', - 'topten':'', - 'viewLegend':'ON', - 'intervalAnalystCheck':'ON', - 'valsHidden':'OFF', - 'database':'', - 'criteria':None, - 'MDPChoice':None, - 'bootCheck':None, - 'permCheck':None, - 'applyVarianceSE':None, - 'strainNames':'_', - 'strainVals':'_', - 'strainVars':'_', - 'otherStrainNames':'_', - 'otherStrainVals':'_', - 'otherStrainVars':'_', - 'extra_attributes':'_', - 'other_extra_attributes':'_' - } - - if fd.enablevariance: - hddn['enablevariance']='ON' - if fd.incparentsf1: - hddn['incparentsf1']='ON' - - if thisTrait: - hddn['fullname'] = str(thisTrait) - try: - hddn['normalPlotTitle'] = thisTrait.symbol - hddn['normalPlotTitle'] += ": " - hddn['normalPlotTitle'] += thisTrait.name - except: - hddn['normalPlotTitle'] = str(thisTrait.name) - hddn['fromDataEditingPage'] = 1 - if thisTrait.db and thisTrait.db.type and thisTrait.db.type == 'ProbeSet': - hddn['trait_type'] = thisTrait.db.type - if thisTrait.cellid: - hddn['cellid'] = thisTrait.cellid - else: - self.cursor.execute("SELECT h2 from ProbeSetXRef WHERE DataId = %d" % thisTrait.mysqlid) - heritability = self.cursor.fetchone() - hddn['heritability'] = heritability - - hddn['attribute_names'] = "" - - hddn['mappingMethodId'] = webqtlDatabaseFunction.getMappingMethod (cursor=self.cursor, groupName=fd.RISet) - - ############################# - ## Display Trait Information - ############################# - - #headSpan = self.dispHeader(fd,thisTrait) #Draw header - # - #titleTop.append(headSpan) - - if fd.identification: - hddn['identification'] = fd.identification - - else: - hddn['identification'] = "Un-named trait" #If no identification, set identification to un-named - - self.dispTraitInformation(fd, "", hddn, thisTrait) #Display trait information + function buttons - - ############################# - ## Generate form and buttons - ############################# - - mainForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), - name='dataInput', submit=HT.Input(type='hidden')) - - next=HT.Input(type='submit', name='submit',value='Next',Class="button") - reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button") - correlationMenus = [] - - if thisTrait == None: - thisTrait = webqtlTrait(data=fd.allTraitData, db=None) - - # Variance submit page only - if fd.enablevariance and not varianceDataPage: - title2Body.append("Click the next button to go to the variance submission form.", - HT.Center(next,reset)) - else: - self.dispBasicStatistics(fd, title2Body, thisTrait) - self.dispCorrelationTools(fd, title3Body, thisTrait) - self.dispMappingTools(fd, title4Body, thisTrait) - - ############################# - ## Trait Value Table - ############################# - - self.dispTraitValues(fd, title5Body, varianceDataPage, nCols, mainForm, thisTrait) - - if fd.allstrainlist: - hddn['allstrainlist'] = string.join(fd.allstrainlist, ' ') - for key in hddn.keys(): - mainForm.append(HT.Input(name=key, value=hddn[key], type='hidden')) - - if fd.enablevariance and not varianceDataPage: - #pre dataediting page, need to submit variance - mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body) - else: - mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body) - TD_LR.append(HT.Paragraph(mainForm)) - self.dict['body'] = str(TD_LR) - - ########################################## - ## Function to display header - ########################################## - def dispHeader(self, fd, thisTrait): - headSpan = HT.Div(style="font-size:14px;") - - #If trait, use trait name; otherwise, use identification value - if thisTrait: - if thisTrait.cellid: - headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Probe ID ', thisTrait.cellid) - else: - headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Record ID ', thisTrait.name) - else: - if fd.identification: - headSpan.append(HT.Strong('Trait ID ', style='font-size:16px;'),fd.identification) - else: - headSpan.append(HT.Strong('Un-named Trait', style='font-size:16px;')) - - return headSpan - - ########################################## - ## Function to display trait infos - ########################################## - def dispTraitInformation(self, fd, title1Body, hddn, thisTrait): - - _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) - - #tbl = HT.TableLite(cellpadding=2, Class="collap", style="margin-left:20px;", width="840", valign="top", id="target1") - - #reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button") - - #XZ, August 02, 2011: The display of icons is decided by the trait type (if trait exists), along with user log-in status. Note that the new submitted trait might not be trait object. - addSelectionButton = "" - verifyButton = "" - rnaseqButton = "" - geneWikiButton = "" - probeButton = "" - similarButton = "" - snpBrowserButton = "" - updateButton = "" - - addSelectionText = "" - verifyText = "" - rnaseqText = "" - geneWikiText = "" - probeText = "" - similarText = "" - snpBrowserText = "" - updateText = "" - - if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']: - - if thisTrait==None or thisTrait.db.type=='Temp': - updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'addPublish');") - updateButton_img = HT.Image("/images/edit_icon.jpg", name="addnew", alt="Add To Publish", title="Add To Publish", style="border:none;") - updateButton.append(updateButton_img) - updateText = "Edit" - elif thisTrait.db.type != 'Temp': - if thisTrait.db.type == 'Publish' and thisTrait.confidential: #XZ: confidential phenotype trait - if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users): - updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") - updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") - updateButton.append(updateButton_img) - updateText = "Edit" - else: - updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") - updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") - updateButton.append(updateButton_img) - updateText = "Edit" - else: - pass - - self.cursor.execute('SELECT Name FROM InbredSet WHERE Name="%s"' % fd.RISet) - if thisTrait: - addSelectionButton = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (fd.RISet, 'dataInput')) - addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;") - #addSelectionButton.append(addSelectionButton_img) - addSelectionText = "Add" - elif self.cursor.fetchall(): - addSelectionButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('%s')[0], 'addRecord');" % ('dataInput')) - addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="", alt="Add To Collection", title="Add To Collection", style="border:none;") - #addSelectionButton.append(addSelectionButton_img) - addSelectionText = "Add" - else: - pass - - - # Microarray database information to display - if thisTrait and thisTrait.db and thisTrait.db.type == 'ProbeSet': #before, this line was only reached if thisTrait != 0, but now we need to check - try: - hddn['GeneId'] = int(string.strip(thisTrait.geneid)) - except: - pass - - #Info2Disp = HT.Paragraph() - - #XZ: Gene Symbol - if thisTrait.symbol: - #XZ: Show SNP Browser only for mouse - if _Species == 'mouse': - self.cursor.execute("select geneSymbol from GeneList where geneSymbol = %s", thisTrait.symbol) - geneName = self.cursor.fetchone() - if geneName: - snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + "&geneName=%s" % geneName[0] - else: - if thisTrait.chr and thisTrait.mb: - snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + \ - "&chr=%s&start=%2.6f&end=%2.6f" % (thisTrait.chr, thisTrait.mb-0.002, thisTrait.mb+0.002) - else: - snpurl = "" - - if snpurl: - snpBrowserButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % snpurl) - snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="snpbrowser", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;") - snpBrowserButton.append(snpBrowserButton_img) - snpBrowserText = "SNPs" - - #XZ: Show GeneWiki for all species - geneWikiButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + "?FormID=geneWiki&symbol=%s" % thisTrait.symbol)) - geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="genewiki", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;") - geneWikiButton.append(geneWikiButton_img) - geneWikiText = 'GeneWiki' - - #XZ: display similar traits in other selected datasets - if thisTrait and thisTrait.db and thisTrait.db.type=="ProbeSet" and thisTrait.symbol: - if _Species in ("mouse", "rat", "human"): - similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.symbol, _Species) - similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl) - similarButton_img = HT.Image("/images/find_icon.jpg", name="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;") - similarButton.append(similarButton_img) - similarText = "Find" - else: - pass - tbl.append(HT.TR( - HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span('%s' % thisTrait.symbol, valign="top", Class="fs13 fsI"), valign="top", width=740) - )) - else: - tbl.append(HT.TR( - HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span('Not available', Class="fs13 fsI"), valign="top") - )) - - #XZ: Gene Alias - if thisTrait.alias: - alias = string.replace(thisTrait.alias, ";", " ") - alias = string.join(string.split(alias), ", ") - tbl.append(HT.TR( - HT.TD('Aliases: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(alias, Class="fs13 fsI"), valign="top") - )) - - #XZ: Description - if thisTrait.description: - tSpan = HT.Span(thisTrait.description, Class="fs13") - if thisTrait.probe_target_description: - tSpan.append('; ', thisTrait.probe_target_description) - else: - tSpan = HT.Span('Not available', Class="fs13") - tbl.append(HT.TR( - HT.TD('Description: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top") - )) - - #XZ: Location - - #XZ: deal with Chr and Mb - if thisTrait.chr and thisTrait.mb: - tSpan = HT.Span('Chr %s @ %s Mb' % (thisTrait.chr,thisTrait.mb),Class="fs13") - elif (thisTrait.chr): - tSpan = HT.Span('Chr %s @ Unknown position' % (thisTrait.chr), Class="fs13") - else: - tSpan = HT.Span('Not available', Class="fs13") - - #XZ: deal with direction - if thisTrait.strand_probe == '+': - tSpan.append(' on the plus strand ') - elif thisTrait.strand_probe == '-': - tSpan.append(' on the minus strand ') - else: - pass - - tbl.append(HT.TR( - HT.TD('Location: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top") - )) - - ##display Verify Location button - try: - blatsequence = thisTrait.blatseq - if not blatsequence: - #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. - self.cursor.execute("""SELECT Probe.Sequence, Probe.Name - FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSet.Name = '%s' AND - Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (thisTrait.db.name, thisTrait.name) ) - seqs = self.cursor.fetchall() - if not seqs: - raise ValueError - else: - blatsequence = '' - for seqt in seqs: - if int(seqt[1][-1]) % 2 == 1: - blatsequence += string.strip(seqt[0]) - - #--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe - blatsequence = '%3E'+thisTrait.name+'%0A'+blatsequence+'%0A' - #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. - self.cursor.execute("""SELECT Probe.Sequence, Probe.Name - FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSet.Name = '%s' AND - Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (thisTrait.db.name, thisTrait.name) ) - - seqs = self.cursor.fetchall() - for seqt in seqs: - if int(seqt[1][-1]) %2 == 1: - blatsequence += '%3EProbe_'+string.strip(seqt[1])+'%0A'+string.strip(seqt[0])+'%0A' - #-------- - #XZ, 07/16/2009: targetsequence is not used, so I comment out this block - #targetsequence = thisTrait.targetseq - #if targetsequence==None: - # targetsequence = "" - - #XZ: Pay attention to the parameter of version (rn, mm, hg). They need to be changed if necessary. - if _Species == "rat": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence) - UTHSC_BLAT_URL = "" - elif _Species == "mouse": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence) - UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', blatsequence) - elif _Species == "human": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) - UTHSC_BLAT_URL = "" - else: - UCSC_BLAT_URL = "" - UTHSC_BLAT_URL = "" - - if UCSC_BLAT_URL: - verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL) - verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", - title=" Check probe locations at UCSC ", style="border:none;") - verifyButton.append(verifyButtonImg) - verifyText = 'Verify' - if UTHSC_BLAT_URL: - rnaseqButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UTHSC_BLAT_URL) - rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", - title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") - rnaseqButton.append(rnaseqButtonImg) - rnaseqText = 'RNA-seq' - tSpan.append(HT.BR()) - except: - pass - - #Display probe information (if any) - if thisTrait.db.name.find('Liver') >= 0 and thisTrait.db.name.find('F2') < 0: - pass - else: - #query database for number of probes associated with trait; if count > 0, set probe tool button and text - self.cursor.execute("""SELECT count(*) - FROM Probe, ProbeSet - WHERE ProbeSet.Name = '%s' AND Probe.ProbeSetId = ProbeSet.Id""" % (thisTrait.name)) - - probeResult = self.cursor.fetchone() - if probeResult[0] > 0: - probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&RISet=%s&incparentsf1=ON" \ - % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.db, thisTrait.name, thisTrait.cellid, fd.RISet) - probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl) - probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;") - probeButton.append(probeButton_img) - probeText = "Probes" - - tSpan = HT.Span(Class="fs13") - - #XZ: deal with blat score and blat specificity. - if thisTrait.probe_set_specificity or thisTrait.probe_set_blat_score: - if thisTrait.probe_set_specificity: - tSpan.append(HT.Href(url="/blatInfo.html", target="_blank", title="Values higher than 2 for the specificity are good", text="BLAT specificity", Class="non_bold"),": %.1f" % float(thisTrait.probe_set_specificity), " "*3) - if thisTrait.probe_set_blat_score: - tSpan.append("Score: %s" % int(thisTrait.probe_set_blat_score), " "*2) - - onClick="openNewWin('/blatInfo.html')" - - tbl.append(HT.TR( - HT.TD('Target Score: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top") - )) - - tSpan = HT.Span(Class="fs13") - tSpan.append(str(_Species).capitalize(), ", ", fd.RISet) - - tbl.append(HT.TR( - HT.TD('Species and Group: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top") - )) - - if thisTrait.cellid: - self.cursor.execute(""" - select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze - where - ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND - ProbeSetFreeze.Id = %d""" % thisTrait.db.id) - probeDBName = self.cursor.fetchone()[0] - tbl.append(HT.TR( - HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span('%s' % probeDBName, Class="non_bold"), valign="top") - )) - else: - tbl.append(HT.TR( - HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name, - target='_blank', Class="fs13 fwn non_bold"), valign="top") - )) - - #XZ: ID links - if thisTrait.genbankid or thisTrait.geneid or thisTrait.unigeneid or thisTrait.omim or thisTrait.homologeneid: - idStyle = "background:#dddddd;padding:2" - tSpan = HT.Span(Class="fs13") - if thisTrait.geneid: - gurl = HT.Href(text= 'Gene', target='_blank',\ - url=webqtlConfig.NCBI_LOCUSID % thisTrait.geneid, Class="fs14 fwn", title="Info from NCBI Entrez Gene") - tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - if thisTrait.omim: - gurl = HT.Href(text= 'OMIM', target='_blank', \ - url= webqtlConfig.OMIM_ID % thisTrait.omim,Class="fs14 fwn", title="Summary from On Mendelian Inheritance in Man") - tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - if thisTrait.unigeneid: - try: - gurl = HT.Href(text= 'UniGene',target='_blank',\ - url= webqtlConfig.UNIGEN_ID % tuple(string.split(thisTrait.unigeneid,'.')[:2]),Class="fs14 fwn", title="UniGene ID") - tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - except: - pass - if thisTrait.genbankid: - thisTrait.genbankid = '|'.join(thisTrait.genbankid.split('|')[0:10]) - if thisTrait.genbankid[-1]=='|': - thisTrait.genbankid=thisTrait.genbankid[0:-1] - gurl = HT.Href(text= 'GenBank', target='_blank', \ - url= webqtlConfig.GENBANK_ID % thisTrait.genbankid,Class="fs14 fwn", title="Find the original GenBank sequence used to design the probes") - tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - if thisTrait.homologeneid: - hurl = HT.Href(text= 'HomoloGene', target='_blank',\ - url=webqtlConfig.HOMOLOGENE_ID % thisTrait.homologeneid, Class="fs14 fwn", title="Find similar genes in other species") - tSpan.append(HT.Span(hurl, style=idStyle), " "*2) - - tbl.append( - HT.TR(HT.TD(colspan=3,height=6)), - HT.TR( - HT.TD('Resource Links: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top") - )) - - #XZ: Resource Links: - if thisTrait.symbol: - linkStyle = "background:#dddddd;padding:2" - tSpan = HT.Span(style="font-family:verdana,serif;font-size:13px") - - #XZ,12/26/2008: Gene symbol may contain single quotation mark. - #For example, Affymetrix, mouse430v2, 1440338_at, the symbol is 2'-Pde (geneid 211948) - #I debug this by using double quotation marks. - if _Species == "rat": - - #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more - #symatlas_species = "Rattus norvegicus" - - #self.cursor.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = '%s'" % thisTrait.symbol) - self.cursor.execute('SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = "%s"' % thisTrait.symbol) - try: - kgId, chr, txst, txen = self.cursor.fetchall()[0] - if chr and txst and txen and kgId: - txst = int(txst*1000000) - txen = int(txen*1000000) - tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\ - title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('rn3',kgId,chr,txst,txen),Class="fs14 fwn"), style=linkStyle) - , " "*2) - except: - pass - if _Species == "mouse": - - #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more - #symatlas_species = "Mus musculus" - - #self.cursor.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = '%s'" % thisTrait.symbol) - self.cursor.execute('SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = "%s"' % thisTrait.symbol) - try: - chr, txst, txen = self.cursor.fetchall()[0] - if chr and txst and txen and thisTrait.refseq_transcriptid : - txst = int(txst*1000000) - txen = int(txen*1000000) - tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\ - title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('mm9',thisTrait.refseq_transcriptid,chr,txst,txen), - Class="fs14 fwn"), style=linkStyle) - , " "*2) - except: - pass - - #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more - #tSpan.append(HT.Span(HT.Href(text= 'SymAtlas',target="mainFrame",\ - # url="http://symatlas.gnf.org/SymAtlas/bioentry?querytext=%s&query=14&species=%s&type=Expression" \ - # % (thisTrait.symbol,symatlas_species),Class="fs14 fwn", \ - # title="Expression across many tissues and cell types"), style=linkStyle), " "*2) - if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"): - tSpan.append(HT.Span(HT.Href(text= 'BioGPS',target="mainFrame",\ - url="http://biogps.gnf.org/?org=%s#goto=genereport&id=%s" \ - % (_Species, thisTrait.geneid),Class="fs14 fwn", \ - title="Expression across many tissues and cell types"), style=linkStyle), " "*2) - tSpan.append(HT.Span(HT.Href(text= 'STRING',target="mainFrame",\ - url="http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=%s" \ - % thisTrait.symbol,Class="fs14 fwn", \ - title="Protein interactions: known and inferred"), style=linkStyle), " "*2) - if thisTrait.symbol: - #ZS: The "species scientific" converts the plain English species names we're using to their scientific names, which are needed for PANTHER's input - #We should probably use the scientific name along with the English name (if not instead of) elsewhere as well, given potential non-English speaking users - if _Species == "mouse": - species_scientific = "Mus%20musculus" - elif _Species == "rat": - species_scientific = "Rattus%20norvegicus" - elif _Species == "human": - species_scientific = "Homo%20sapiens" - elif _Species == "drosophila": - species_scientific = "Drosophila%20melanogaster" - else: - species_scientific = "all" - - species_scientific - tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \ - url="http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=%s&listType=1&fieldValue=%s" \ - % (species_scientific, thisTrait.symbol),Class="fs14 fwn", \ - title="Gene and protein data resources from Celera-ABI"), style=linkStyle), " "*2) - else: - pass - #tSpan.append(HT.Span(HT.Href(text= 'BIND',target="mainFrame",\ - # url="http://bind.ca/?textquery=%s" \ - # % thisTrait.symbol,Class="fs14 fwn", \ - # title="Protein interactions"), style=linkStyle), " "*2) - if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"): - tSpan.append(HT.Span(HT.Href(text= 'Gemma',target="mainFrame",\ - url="http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" \ - % thisTrait.geneid, Class="fs14 fwn", \ - title="Meta-analysis of gene expression data"), style=linkStyle), " "*2) - tSpan.append(HT.Span(HT.Href(text= 'SynDB',target="mainFrame",\ - url="http://lily.uthsc.edu:8080/20091027_GNInterfaces/20091027_redirectSynDB.jsp?query=%s" \ - % thisTrait.symbol, Class="fs14 fwn", \ - title="Brain synapse database"), style=linkStyle), " "*2) - if _Species == "mouse": - tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ - url="http://mouse.brain-map.org/brain/%s.html" \ - % thisTrait.symbol, Class="fs14 fwn", \ - title="Allen Brain Atlas"), style=linkStyle), " "*2) - - if thisTrait.geneid: - #if _Species == "mouse": - # tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ - # url="http://www.brain-map.org/search.do?queryText=egeneid=%s" \ - # % thisTrait.geneid, Class="fs14 fwn", \ - # title="Allen Brain Atlas"), style=linkStyle), " "*2) - if _Species == "human": - tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ - url="http://humancortex.alleninstitute.org/has/human/imageseries/search/1.html?searchSym=t&searchAlt=t&searchName=t&gene_term=&entrez_term=%s" \ - % thisTrait.geneid, Class="fs14 fwn", \ - title="Allen Brain Atlas"), style=linkStyle), " "*2) - tbl.append( - HT.TR(HT.TD(colspan=3,height=6)), - HT.TR( - HT.TD(' '), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top"))) - - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="620", id="target1") - menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(similarButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(geneWikiButton, align="center"),HT.TD(snpBrowserButton, align="center"),HT.TD(rnaseqButton, align="center"),HT.TD(probeButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(similarText, align="center"),HT.TD(verifyText, align="center"),HT.TD(geneWikiText, align="center"),HT.TD(snpBrowserText, align="center"),HT.TD(rnaseqText, align="center"),HT.TD(probeText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - - - #for zhou mi's cliques, need to be removed - #if self.database[:6] == 'BXDMic' and self.ProbeSetID in cliqueID: - # Info2Disp.append(HT.Strong('Clique Search: '),HT.Href(text='Search',\ - # url ="http://compbio1.utmem.edu/clique_go/results.php?pid=%s&pval_1=0&pval_2=0.001" \ - # % self.ProbeSetID,target='_blank',Class="normalsize"),HT.BR()) - - #linkTable.append(HT.TR(linkTD)) - #Info2Disp.append(linkTable) - title1Body.append(tbl, HT.BR(), menuTable) - - elif thisTrait and thisTrait.db and thisTrait.db.type =='Publish': #Check if trait is phenotype - - if thisTrait.confidential: - tbl.append(HT.TR( - HT.TD('Pre-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.pre_publication_description, Class="fs13"), valign="top", width=740) - )) - if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users): - tbl.append(HT.TR( - HT.TD('Post-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Pre-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.pre_publication_abbreviation, Class="fs13"), valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Post-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.post_publication_abbreviation, Class="fs13"), valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Lab code: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.lab_code, Class="fs13"), valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Owner: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.owner, Class="fs13"), valign="top", width=740) - )) - else: - tbl.append(HT.TR( - HT.TD('Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Authors: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.authors, Class="fs13"), - valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Title: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.title, Class="fs13"), - valign="top", width=740) - )) - if thisTrait.journal: - journal = thisTrait.journal - if thisTrait.year: - journal = thisTrait.journal + " (%s)" % thisTrait.year - - tbl.append(HT.TR( - HT.TD('Journal: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(journal, Class="fs13"), - valign="top", width=740) - )) - PubMedLink = "" - if thisTrait.pubmed_id: - PubMedLink = webqtlConfig.PUBMEDLINK_URL % thisTrait.pubmed_id - if PubMedLink: - tbl.append(HT.TR( - HT.TD('Link: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(HT.Href(url=PubMedLink, text="PubMed",target='_blank',Class="fs14 fwn"), - style = "background:#cddcff;padding:2"), valign="top", width=740) - )) - - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1") - menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - - title1Body.append(tbl, HT.BR(), menuTable) - - elif thisTrait and thisTrait.db and thisTrait.db.type == 'Geno': #Check if trait is genotype - - GenoInfo = HT.Paragraph() - if thisTrait.chr and thisTrait.mb: - location = ' Chr %s @ %s Mb' % (thisTrait.chr,thisTrait.mb) - else: - location = "not available" - - if thisTrait.sequence and len(thisTrait.sequence) > 100: - if _Species == "rat": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', thisTrait.sequence) - UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('rat', 'rn3', thisTrait.sequence) - elif _Species == "mouse": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', thisTrait.sequence) - UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', thisTrait.sequence) - elif _Species == "human": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) - UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('human', 'hg19', thisTrait.sequence) - else: - UCSC_BLAT_URL = "" - UTHSC_BLAT_URL = "" - if UCSC_BLAT_URL: - #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL) - verifyButton = HT.Href(url="#") - verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;") - verifyButton.append(verifyButtonImg) - verifyText = "Verify" - rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL) - rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") - rnaseqButton.append(rnaseqButtonImg) - rnaseqText = "RNA-seq" - - tbl.append(HT.TR( - HT.TD('Location: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(location, Class="fs13"), valign="top", width=740) - ), - HT.TR( - HT.TD('SNP Search: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp&cmd=search&term=%s" % thisTrait.name, 'NCBI',Class="fs13"), - valign="top", width=740) - )) - - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="275", id="target1") - menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(rnaseqButton, align="center"), HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(verifyText, align="center"),HT.TD(rnaseqText, align="center"), HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - - title1Body.append(tbl, HT.BR(), menuTable) - - elif (thisTrait == None or thisTrait.db.type == 'Temp'): #if temporary trait (user-submitted trait or PCA trait) - - TempInfo = HT.Paragraph() - if thisTrait != None: - if thisTrait.description: - tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),' %s ' % thisTrait.description,HT.BR()), colspan=3, height=15)) - else: - tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),'not available',HT.BR(),HT.BR()), colspan=3, height=15)) - - if (updateText == "Edit"): - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1") - else: - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="80", id="target1") - - menuTable.append(HT.TR(HT.TD(addSelectionButton, align="right"),HT.TD(updateButton, align="right"), colspan=3, height=50, style="vertical-align:bottom;") ) - menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - - title1Body.append(tbl, HT.BR(), menuTable) - - else: - pass - - - ########################################## - ## Function to display analysis tools - ########################################## - def dispBasicStatistics(self, fd, title2Body, thisTrait): - - #XZ, June 22, 2011: The definition and usage of primary_strains, other_strains, specialStrains, all_strains are not clear and hard to understand. But since they are only used in this function for draw graph purpose, they will not hurt the business logic outside. As of June 21, 2011, this function seems work fine, so no hurry to clean up. These parameters and code in this function should be cleaned along with fd.f1list, fd.parlist, fd.strainlist later. - stats_row = HT.TR() - stats_cell = HT.TD() - - if fd.genotype.type == "riset": - strainlist = fd.f1list + fd.strainlist - else: - strainlist = fd.f1list + fd.parlist + fd.strainlist - - other_strains = [] #XZ: strain that is not of primary group - specialStrains = [] #XZ: This might be replaced by other_strains / ZS: It is just other strains without parent/f1 strains. - all_strains = [] - primary_strains = [] #XZ: strain of primary group, e.g., BXD, LXS - - MDP_menu = HT.Select(name='stats_mdp', Class='stats_mdp') - - for strain in thisTrait.data.keys(): - strainName = strain.replace("_2nd_", "") - if strain not in strainlist: - if (thisTrait.data[strainName].val != None): - if strain.find('F1') < 0: - specialStrains.append(strain) - if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)): - other_strains.append(strain) #XZ: at current stage, other_strains doesn't include parent strains and F1 strains of primary group - else: - if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)): - primary_strains.append(strain) #XZ: at current stage, the primary_strains is the same as fd.strainlist / ZS: I tried defining primary_strains as fd.strainlist instead, but in some cases it ended up including the parent strains (1436869_at BXD) - - if len(other_strains) > 3: - other_strains.sort(key=webqtlUtil.natsort_key) - primary_strains.sort(key=webqtlUtil.natsort_key) - primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains #XZ: note that fd.f1list and fd.parlist are added. - all_strains = primary_strains + other_strains - other_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_strains #XZ: note that fd.f1list and fd.parlist are added. - MDP_menu.append(('All Cases','0')) - MDP_menu.append(('%s Only' % fd.RISet,'1')) - MDP_menu.append(('Non-%s Only' % fd.RISet,'2')) - stats_row.append("Include: ", MDP_menu, HT.BR(), HT.BR()) - else: - if (len(other_strains) > 0) and (len(primary_strains) + len(other_strains) > 3): - MDP_menu.append(('All Cases','0')) - MDP_menu.append(('%s Only' % fd.RISet,'1')) - MDP_menu.append(('Non-%s Only' % fd.RISet,'2')) - stats_row.append("Include: ", MDP_menu, " "*3) - all_strains = primary_strains - all_strains.sort(key=webqtlUtil.natsort_key) - all_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + all_strains - primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains - else: - all_strains = strainlist - - other_strains.sort(key=webqtlUtil.natsort_key) - all_strains = all_strains + other_strains - pass - - update_button = HT.Input(type='button',value=' Update Figures ', Class="button update") #This is used to reload the page and update the Basic Statistics figures with user-edited data - stats_row.append(update_button, HT.BR(), HT.BR()) - - if (len(other_strains)) > 0 and (len(primary_strains) + len(other_strains) > 4): - #One set of vals for all, selected strain only, and non-selected only - vals1 = [] - vals2 = [] - vals3 = [] - - #Using all strains/cases for values - for i, strainNameOrig in enumerate(all_strains): - strainName = strainNameOrig.replace("_2nd_", "") - - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue - - vals1.append(thisValFull) - - #Using just the RISet strain - for i, strainNameOrig in enumerate(primary_strains): - strainName = strainNameOrig.replace("_2nd_", "") - - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue - - vals2.append(thisValFull) - - #Using all non-RISet strains only - for i, strainNameOrig in enumerate(other_strains): - strainName = strainNameOrig.replace("_2nd_", "") - - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue - - vals3.append(thisValFull) - - vals_set = [vals1,vals2,vals3] - - else: - vals = [] - - #Using all strains/cases for values - for i, strainNameOrig in enumerate(all_strains): - strainName = strainNameOrig.replace("_2nd_", "") - - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue - - vals.append(thisValFull) - - vals_set = [vals] - - stats_script = HT.Script(language="Javascript") #script needed for tabs - - for i, vals in enumerate(vals_set): - if i == 0 and len(vals) < 4: - stats_container = HT.Div(id="stats_tabs", style="padding:10px;", Class="ui-tabs") #Needed for tabs; notice the "stats_script_text" below referring to this element - stats_container.append(HT.Div(HT.Italic("Fewer than 4 case data were entered. No statistical analysis has been attempted."))) - stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" - stats_cell.append(stats_container) - break - elif (i == 1 and len(primary_strains) < 4): - stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") - stats_container.append(HT.Div(HT.Italic("Fewer than 4 " + fd.RISet + " case data were entered. No statistical analysis has been attempted."))) - elif (i == 2 and len(other_strains) < 4): - stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") - stats_container.append(HT.Div(HT.Italic("Fewer than 4 non-" + fd.RISet + " case data were entered. No statistical analysis has been attempted."))) - stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});""" - else: - stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") - stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});""" - if len(vals) > 4: - stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-5", Class="stats_tab"), - HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"), - HT.Href(text="Box Plot", url="#statstabs-2", Class="stats_tab")] - stats_tabs = HT.List(stats_tab_list) - stats_container.append(stats_tabs) - - table_div = HT.Div(id="statstabs-1") - table_container = HT.Paragraph() - - statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - - if thisTrait.db: - if thisTrait.cellid: - statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=thisTrait.db.type, cellid=thisTrait.cellid) - else: - statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=thisTrait.db.type) - else: - statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals) - - statsTable.append(HT.TR(HT.TD(statsTableCell))) - - table_container.append(statsTable) - table_div.append(table_container) - stats_container.append(table_div) - - normalplot_div = HT.Div(id="statstabs-5") - normalplot_container = HT.Paragraph() - normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - - try: - plotTitle = thisTrait.symbol - plotTitle += ": " - plotTitle += thisTrait.name - except: - plotTitle = str(thisTrait.name) - - normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains) - normalplot.append(HT.TR(HT.TD(normalplot_img))) - normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \ - normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(), - "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", - target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary")))) - normalplot_container.append(normalplot) - normalplot_div.append(normalplot_container) - stats_container.append(normalplot_div) - - boxplot_div = HT.Div(id="statstabs-2") - boxplot_container = HT.Paragraph() - boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals) - boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left"))) - boxplot_container.append(boxplot) - boxplot_div.append(boxplot_container) - stats_container.append(boxplot_div) - - - barName_div = HT.Div(id="statstabs-3") - barName_container = HT.Paragraph() - barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name") - barName.append(HT.TR(HT.TD(barName_img))) - barName_container.append(barName) - barName_div.append(barName_container) - stats_container.append(barName_div) - - barRank_div = HT.Div(id="statstabs-4") - barRank_container = HT.Paragraph() - barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank") - barRank.append(HT.TR(HT.TD(barRank_img))) - barRank_container.append(barRank) - barRank_div.append(barRank_container) - stats_container.append(barRank_div) - - stats_cell.append(stats_container) - - stats_script.append(stats_script_text) - - submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") - stats_row.append(stats_cell) - - submitTable.append(stats_row) - submitTable.append(stats_script) - - title2Body.append(submitTable) - - - def dispCorrelationTools(self, fd, title3Body, thisTrait): - - _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) - - RISetgp = fd.RISet - if RISetgp[:3] == 'BXD': - RISetgp = 'BXD' - - if RISetgp: - sample_correlation = HT.Input(type='button',name='sample_corr', value=' Compute ', Class="button sample_corr") - lit_correlation = HT.Input(type='button',name='lit_corr', value=' Compute ', Class="button lit_corr") - tissue_correlation = HT.Input(type='button',name='tiss_corr', value=' Compute ', Class="button tiss_corr") - methodText = HT.Span("Calculate:", Class="ffl fwb fs12") - - databaseText = HT.Span("Database:", Class="ffl fwb fs12") - databaseMenu1 = HT.Select(name='database1') - databaseMenu2 = HT.Select(name='database2') - databaseMenu3 = HT.Select(name='database3') - - nmenu = 0 - self.cursor.execute('SELECT PublishFreeze.FullName,PublishFreeze.Name FROM \ - PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id \ - and InbredSet.Name = "%s" and PublishFreeze.public > %d' % \ - (RISetgp,webqtlConfig.PUBLICTHRESH)) - for item in self.cursor.fetchall(): - databaseMenu1.append(item) - databaseMenu2.append(item) - databaseMenu3.append(item) - nmenu += 1 - self.cursor.execute('SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze,\ - InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = \ - "%s" and GenoFreeze.public > %d' % (RISetgp,webqtlConfig.PUBLICTHRESH)) - for item in self.cursor.fetchall(): - databaseMenu1.append(item) - databaseMenu2.append(item) - databaseMenu3.append(item) - nmenu += 1 - #03/09/2009: Xiaodong changed the SQL query to order by Name as requested by Rob. - self.cursor.execute('SELECT Id, Name FROM Tissue order by Name') - for item in self.cursor.fetchall(): - TId, TName = item - databaseMenuSub = HT.Optgroup(label = '%s ------' % TName) - self.cursor.execute('SELECT ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze, \ - InbredSet WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = %d and \ - ProbeSetFreeze.public > %d and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like "%s%%" \ - order by ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId ' % (TId,webqtlConfig.PUBLICTHRESH, RISetgp)) - for item2 in self.cursor.fetchall(): - databaseMenuSub.append(item2) - nmenu += 1 - databaseMenu1.append(databaseMenuSub) - databaseMenu2.append(databaseMenuSub) - databaseMenu3.append(databaseMenuSub) - if nmenu: - if thisTrait and thisTrait.db != None: - databaseMenu1.selected.append(thisTrait.db.fullname) - databaseMenu2.selected.append(thisTrait.db.fullname) - databaseMenu3.selected.append(thisTrait.db.fullname) - - criteriaText = HT.Span("Return:", Class="ffl fwb fs12") - - criteriaMenu1 = HT.Select(name='criteria1', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") - criteriaMenu1.append(('top 100','100')) - criteriaMenu1.append(('top 200','200')) - criteriaMenu1.append(('top 500','500')) - criteriaMenu1.append(('top 1000','1000')) - criteriaMenu1.append(('top 2000','2000')) - criteriaMenu1.append(('top 5000','5000')) - criteriaMenu1.append(('top 10000','10000')) - criteriaMenu1.append(('top 15000','15000')) - criteriaMenu1.append(('top 20000','20000')) - - criteriaMenu2 = HT.Select(name='criteria2', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") - criteriaMenu2.append(('top 100','100')) - criteriaMenu2.append(('top 200','200')) - criteriaMenu2.append(('top 500','500')) - criteriaMenu2.append(('top 1000','1000')) - criteriaMenu2.append(('top 2000','2000')) - criteriaMenu2.append(('top 5000','5000')) - criteriaMenu2.append(('top 10000','10000')) - criteriaMenu2.append(('top 15000','15000')) - criteriaMenu2.append(('top 20000','20000')) - - criteriaMenu3 = HT.Select(name='criteria3', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") - criteriaMenu3.append(('top 100','100')) - criteriaMenu3.append(('top 200','200')) - criteriaMenu3.append(('top 500','500')) - criteriaMenu3.append(('top 1000','1000')) - criteriaMenu3.append(('top 2000','2000')) - criteriaMenu3.append(('top 5000','5000')) - criteriaMenu3.append(('top 10000','10000')) - criteriaMenu3.append(('top 15000','15000')) - criteriaMenu3.append(('top 20000','20000')) - - - self.MDPRow1 = HT.TR(Class='mdp1') - self.MDPRow2 = HT.TR(Class='mdp2') - self.MDPRow3 = HT.TR(Class='mdp3') - - correlationMenus1 = HT.TableLite( - HT.TR(HT.TD(databaseText), HT.TD(databaseMenu1, colspan="3")), - HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu1)), - self.MDPRow1, cellspacing=0, width="619px", cellpadding=2) - correlationMenus1.append(HT.Input(name='orderBy', value='2', type='hidden')) # to replace the orderBy menu - correlationMenus2 = HT.TableLite( - HT.TR(HT.TD(databaseText), HT.TD(databaseMenu2, colspan="3")), - HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu2)), - self.MDPRow2, cellspacing=0, width="619px", cellpadding=2) - correlationMenus2.append(HT.Input(name='orderBy', value='2', type='hidden')) - correlationMenus3 = HT.TableLite( - HT.TR(HT.TD(databaseText), HT.TD(databaseMenu3, colspan="3")), - HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu3)), - self.MDPRow3, cellspacing=0, width="619px", cellpadding=2) - correlationMenus3.append(HT.Input(name='orderBy', value='2', type='hidden')) - - else: - correlationMenus = "" - - - corr_row = HT.TR() - corr_container = HT.Div(id="corr_tabs", Class="ui-tabs") - - if (thisTrait.db != None and thisTrait.db.type =='ProbeSet'): - corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1"), HT.Href(text='Literature r', url="#corrtabs-2"), HT.Href(text='Tissue r', url="#corrtabs-3")] - else: - corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1")] - - corr_tabs = HT.List(corr_tab_list) - corr_container.append(corr_tabs) - - if correlationMenus1 or correlationMenus2 or correlationMenus3: - sample_div = HT.Div(id="corrtabs-1") - sample_container = HT.Span() - - sample_type = HT.Input(type="radio", name="sample_method", value="1", checked="checked") - sample_type2 = HT.Input(type="radio", name="sample_method", value="2") - - sampleTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - sampleTD = HT.TD(correlationMenus1, HT.BR(), - "Pearson", sample_type, " "*3, "Spearman Rank", sample_type2, HT.BR(), HT.BR(), - sample_correlation, HT.BR(), HT.BR()) - - sampleTD.append(HT.Span("The ",HT.Href(url="/correlationAnnotation.html#sample_r", target="_blank", text="Sample Correlation")," is computed between trait data and", - " any ",HT.BR()," other traits in the sample database selected above. Use ", - HT.Href(url="/glossary.html#Correlations", target="_blank", text="Spearman Rank"), - HT.BR(),"when the sample size is small (<20) or when there are influential \ - outliers.", HT.BR(),Class="fs12")) - - sampleTable.append(sampleTD) - - sample_container.append(sampleTable) - sample_div.append(sample_container) - corr_container.append(sample_div) - - literature_div = HT.Div(id="corrtabs-2") - literature_container = HT.Span() - - literatureTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - literatureTD = HT.TD(correlationMenus2,HT.BR(),lit_correlation, HT.BR(), HT.BR()) - literatureTD.append(HT.Span("The ", HT.Href(url="/correlationAnnotation.html", target="_blank",text="Literature Correlation"), " (Lit r) between this gene and all other genes is computed",HT.BR(), - "using the ", HT.Href(url="https://grits.eecs.utk.edu/sgo/sgo.html", target="_blank", text="Semantic Gene Organizer"), - " and human, rat, and mouse data from PubMed. ", HT.BR(),"Values are ranked by Lit r, \ - but Sample r and Tissue r are also displayed.", HT.BR(), HT.BR(), - HT.Href(url="/glossary.html#Literature", target="_blank", text="More on using Lit r"), Class="fs12")) - literatureTable.append(literatureTD) - - literature_container.append(literatureTable) - literature_div.append(literature_container) - - if thisTrait.db != None: - if (thisTrait.db.type =='ProbeSet'): - corr_container.append(literature_div) - - tissue_div = HT.Div(id="corrtabs-3") - tissue_container = HT.Span() - - tissue_type = HT.Input(type="radio", name="tissue_method", value="4", checked="checked") - tissue_type2 = HT.Input(type="radio", name="tissue_method", value="5") - - tissueTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - tissueTD = HT.TD(correlationMenus3,HT.BR(), - "Pearson", tissue_type, " "*3, "Spearman Rank", tissue_type2, HT.BR(), HT.BR(), - tissue_correlation, HT.BR(), HT.BR()) - tissueTD.append(HT.Span("The ", HT.Href(url="/webqtl/main.py?FormID=tissueCorrelation", target="_blank", text="Tissue Correlation"), - " (Tissue r) estimates the similarity of expression of two genes",HT.BR()," or \ - transcripts across different cells, tissues, or organs (",HT.Href(url="/correlationAnnotation.html#tissue_r", target="_blank", text="glossary"),"). \ - Tissue correlations",HT.BR()," are generated by analyzing expression in multiple samples usually taken from \ - single cases.",HT.BR(),HT.Bold("Pearson")," and ",HT.Bold("Spearman Rank")," correlations have been computed for all pairs \ - of genes",HT.BR()," using data from mouse samples.", - HT.BR(), Class="fs12")) - tissueTable.append(tissueTD) - - tissue_container.append(tissueTable) - tissue_div.append(tissue_container) - if thisTrait.db != None: - if (thisTrait.db.type =='ProbeSet'): - corr_container.append(tissue_div) - - corr_row.append(HT.TD(corr_container)) - - corr_script = HT.Script(language="Javascript") - corr_script_text = """$(function() { $("#corr_tabs").tabs(); });""" - corr_script.append(corr_script_text) - - submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target4") - submitTable.append(corr_row) - submitTable.append(corr_script) - - title3Body.append(submitTable) - - - def dispMappingTools(self, fd, title4Body, thisTrait): - - _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) - - RISetgp = fd.RISet - if RISetgp[:3] == 'BXD': - RISetgp = 'BXD' - - #check boxes - one for regular interval mapping, the other for composite - permCheck1= HT.Input(type='checkbox', Class='checkbox', name='permCheck1',checked="on") - bootCheck1= HT.Input(type='checkbox', Class='checkbox', name='bootCheck1',checked=0) - permCheck2= HT.Input(type='checkbox', Class='checkbox', name='permCheck2',checked="on") - bootCheck2= HT.Input(type='checkbox', Class='checkbox', name='bootCheck2',checked=0) - optionbox1 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression1',checked=0) - optionbox2 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression2',checked=0) - optionbox3 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression3',checked=0) - applyVariance1 = HT.Input(name='applyVarianceSE1',type='checkbox', Class='checkbox') - applyVariance2 = HT.Input(name='applyVarianceSE2',type='checkbox', Class='checkbox') - - IntervalMappingButton=HT.Input(type='button' ,name='interval',value=' Compute ', Class="button") - CompositeMappingButton=HT.Input(type='button' ,name='composite',value=' Compute ', Class="button") - MarkerRegressionButton=HT.Input(type='button',name='marker', value=' Compute ', Class="button") - - chrText = HT.Span("Chromosome:", Class="ffl fwb fs12") - - # updated by NL 5-28-2010 - # Interval Mapping - chrMenu = HT.Select(name='chromosomes1') - chrMenu.append(tuple(["All",-1])) - for i in range(len(fd.genotype)): - if len(fd.genotype[i]) > 1: - chrMenu.append(tuple([fd.genotype[i].name,i])) - - #Menu for Composite Interval Mapping - chrMenu2 = HT.Select(name='chromosomes2') - chrMenu2.append(tuple(["All",-1])) - for i in range(len(fd.genotype)): - if len(fd.genotype[i]) > 1: - chrMenu2.append(tuple([fd.genotype[i].name,i])) - - if fd.genotype.Mbmap: - scaleText = HT.Span("Mapping Scale:", Class="ffl fwb fs12") - scaleMenu1 = HT.Select(name='scale1', onChange="checkUncheck(window.document.dataInput.scale1.value, window.document.dataInput.permCheck1, window.document.dataInput.bootCheck1)") - scaleMenu1.append(("Megabase",'physic')) - scaleMenu1.append(("Centimorgan",'morgan')) - scaleMenu2 = HT.Select(name='scale2', onChange="checkUncheck(window.document.dataInput.scale2.value, window.document.dataInput.permCheck2, window.document.dataInput.bootCheck2)") - scaleMenu2.append(("Megabase",'physic')) - scaleMenu2.append(("Centimorgan",'morgan')) - - controlText = HT.Span("Control Locus:", Class="ffl fwb fs12") - controlMenu = HT.Input(type="text", name="controlLocus", Class="controlLocus") - - if fd.genotype.Mbmap: - intMappingMenu = HT.TableLite( - HT.TR(HT.TD(chrText), HT.TD(chrMenu, colspan="3")), - HT.TR(HT.TD(scaleText), HT.TD(scaleMenu1)), - cellspacing=0, width="263px", cellpadding=2) - compMappingMenu = HT.TableLite( - HT.TR(HT.TD(chrText), HT.TD(chrMenu2, colspan="3")), - HT.TR(HT.TD(scaleText), HT.TD(scaleMenu2)), - HT.TR(HT.TD(controlText), HT.TD(controlMenu)), - cellspacing=0, width="325px", cellpadding=2) - else: - intMappingMenu = HT.TableLite( - HT.TR(HT.TD(chrText), HT.TD(chrMenu, colspan="3")), - cellspacing=0, width="263px", cellpadding=2) - compMappingMenu = HT.TableLite( - HT.TR(HT.TD(chrText), HT.TD(chrMenu2, colspan="3")), - HT.TR(HT.TD(controlText), HT.TD(controlMenu)), - cellspacing=0, width="325px", cellpadding=2) - - directPlotButton = "" - directPlotButton = HT.Input(type='button',name='', value=' Compute ',\ - onClick="dataEditingFunc(this.form,'directPlot');",Class="button") - directPlotSortText = HT.Span(HT.Bold("Sort by: "), Class="ffl fwb fs12") - directPlotSortMenu = HT.Select(name='graphSort') - directPlotSortMenu.append(('LRS Full',0)) - directPlotSortMenu.append(('LRS Interact',1)) - directPlotPermuText = HT.Span("Permutation Test (n=500)", Class="ffl fs12") - directPlotPermu = HT.Input(type='checkbox', Class='checkbox',name='directPermuCheckbox', checked="on") - pairScanReturnText = HT.Span(HT.Bold("Return: "), Class="ffl fwb fs12") - pairScanReturnMenu = HT.Select(name='pairScanReturn') - pairScanReturnMenu.append(('top 50','50')) - pairScanReturnMenu.append(('top 100','100')) - pairScanReturnMenu.append(('top 200','200')) - pairScanReturnMenu.append(('top 500','500')) - - pairScanMenus = HT.TableLite( - HT.TR(HT.TD(directPlotSortText), HT.TD(directPlotSortMenu)), - HT.TR(HT.TD(pairScanReturnText), HT.TD(pairScanReturnMenu)), - cellspacing=0, width="232px", cellpadding=2) - - markerSuggestiveText = HT.Span(HT.Bold("Display LRS greater than:"), Class="ffl fwb fs12") - markerSuggestive = HT.Input(name='suggestive', size=5, maxlength=8) - displayAllText = HT.Span(" Display all LRS ", Class="ffl fs12") - displayAll = HT.Input(name='displayAllLRS', type="checkbox", Class='checkbox') - useParentsText = HT.Span(" Use Parents ", Class="ffl fs12") - useParents = optionbox2 - applyVarianceText = HT.Span(" Use Weighted ", Class="ffl fs12") - - markerMenu = HT.TableLite( - HT.TR(HT.TD(markerSuggestiveText), HT.TD(markerSuggestive)), - HT.TR(HT.TD(displayAll,displayAllText)), - HT.TR(HT.TD(useParents,useParentsText)), - HT.TR(HT.TD(applyVariance2,applyVarianceText)), - cellspacing=0, width="263px", cellpadding=2) - - - mapping_row = HT.TR() - mapping_container = HT.Div(id="mapping_tabs", Class="ui-tabs") - - mapping_tab_list = [HT.Href(text="Interval", url="#mappingtabs-1"), HT.Href(text="Marker Regression", url="#mappingtabs-2"), HT.Href(text="Composite", url="#mappingtabs-3"), HT.Href(text="Pair-Scan", url="#mappingtabs-4")] - mapping_tabs = HT.List(mapping_tab_list) - mapping_container.append(mapping_tabs) - - interval_div = HT.Div(id="mappingtabs-1") - interval_container = HT.Span() - - intervalTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - intTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") - intTD.append(intMappingMenu,HT.BR()) - - intTD.append(permCheck1,'Permutation Test (n=2000)',HT.BR(), - bootCheck1,'Bootstrap Test (n=2000)', HT.BR(), optionbox1, 'Use Parents', HT.BR(), - applyVariance1,'Use Weighted', HT.BR(), HT.BR(),IntervalMappingButton, HT.BR(), HT.BR()) - intervalTable.append(HT.TR(intTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#intmap', target='_blank', text='Interval Mapping'), - ' computes linkage maps for the entire genome or single',HT.BR(),' chromosomes.', - ' The ',HT.Href(url='/glossary.html#permutation', target='_blank', text='Permutation Test'),' estimates suggestive and significant ',HT.BR(),' linkage scores. \ - The ',HT.Href(url='/glossary.html#bootstrap', target='_blank', text='Bootstrap Test'), ' estimates the precision of the QTL location.' - ,Class="fs12"), HT.BR(), valign="top"))) - - interval_container.append(intervalTable) - interval_div.append(interval_container) - mapping_container.append(interval_div) - - # Marker Regression - - marker_div = HT.Div(id="mappingtabs-2") - marker_container = HT.Span() - - markerTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - markerTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") - markerTD.append(markerMenu,HT.BR()) - - markerTD.append(MarkerRegressionButton,HT.BR(),HT.BR()) - - markerTable.append(HT.TR(markerTD),HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#',target='_blank',text='Marker regression'), - ' computes and displays LRS values for individual markers.',HT.BR(), - 'This function also lists additive effects (phenotype units per allele) and', HT.BR(), - 'dominance deviations for some datasets.', HT.BR(),Class="fs12"), HT.BR(), valign="top"))) - - marker_container.append(markerTable) - marker_div.append(marker_container) - mapping_container.append(marker_div) - - # Composite interval mapping - composite_div = HT.Div(id="mappingtabs-3") - composite_container = HT.Span() - - compositeTable = HT.TableLite(cellspacing=0, cellpadding=3, width="100%") - compTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") - compTD.append(compMappingMenu,HT.BR()) - - compTD.append(permCheck2, 'Permutation Test (n=2000)',HT.BR(), - bootCheck2,'Bootstrap Test (n=2000)', HT.BR(), - optionbox3, 'Use Parents', HT.BR(), HT.BR(), CompositeMappingButton, HT.BR(), HT.BR()) - compositeTable.append(HT.TR(compTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#Composite',target='_blank',text='Composite Interval Mapping'), - " allows you to control for a single marker as",HT.BR()," a cofactor. ", - "To find a control marker, run the ",HT.Bold("Marker Regression")," function."), - HT.BR(), valign="top"))) - - composite_container.append(compositeTable) - composite_div.append(composite_container) - mapping_container.append(composite_div) - - # Pair Scan - - pairscan_div = HT.Div(id="mappingtabs-4") - pairscan_container = HT.Span() - - pairScanTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - pairScanTD = HT.TD(NOWRAP='ON', Class="fs12 fwn") - pairScanTD.append(pairScanMenus,HT.BR()) - pairScanTD.append(directPlotPermu, directPlotPermuText, HT.BR(), HT.BR(), - directPlotButton,HT.BR(),HT.BR()) - pairScanTable.append(HT.TR(pairScanTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#Pair_Scan', target="_blank", text='Pair-Scan'), - ' searches for pairs of chromosomal regions that are',HT.BR(), - 'involved in two-locus epistatic interactions.'), HT.BR(), valign="top"))) - - pairscan_container.append(pairScanTable) - pairscan_div.append(pairscan_container) - mapping_container.append(pairscan_div) - - mapping_row.append(HT.TD(mapping_container)) - - # Treat Interval Mapping and Marker Regression and Pair Scan as a group for displaying - #disable Interval Mapping and Marker Regression and Pair Scan for human and the dataset doesn't have genotype file - mappingMethodId = webqtlDatabaseFunction.getMappingMethod(cursor=self.cursor, groupName=RISetgp) - - mapping_script = HT.Script(language="Javascript") - mapping_script_text = """$(function() { $("#mapping_tabs").tabs(); });""" - mapping_script.append(mapping_script_text) - - submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") - - if mappingMethodId != None: - if int(mappingMethodId) == 1: - submitTable.append(mapping_row) - submitTable.append(mapping_script) - elif int(mappingMethodId) == 4: - # NL; 09-26-2011 testing for Human Genome Association function - mapping_row=HT.TR() - mapping_container = HT.Div(id="mapping_tabs", Class="ui-tabs") - - mapping_tab_list = [HT.Href(text="Genome Association", url="#mappingtabs-1")] - mapping_tabs = HT.List(mapping_tab_list) - mapping_container.append(mapping_tabs) - - # Genome Association - markerSuggestiveText = HT.Span(HT.Bold("P Value:"), Class="ffl fwb fs12") - - markerSuggestive = HT.Input(name='pValue', value='0.001', size=10, maxlength=20,onClick="this.value='';",onBlur="if(this.value==''){this.value='0.001'};") - markerMenu = HT.TableLite(HT.TR(HT.TD(markerSuggestiveText), HT.TD(markerSuggestive),HT.TD(HT.Italic('   (e.g. 0.001 or 1e-3 or 1E-3 or 3)'))),cellspacing=0, width="400px", cellpadding=2) - MarkerRegressionButton=HT.Input(type='button',name='computePlink', value='  Compute Using PLINK  ', onClick= "validatePvalue(this.form);", Class="button") - - marker_div = HT.Div(id="mappingtabs-1") - marker_container = HT.Span() - markerTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - markerTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") - markerTD.append(markerMenu,HT.BR()) - markerTD.append(MarkerRegressionButton,HT.BR(),HT.BR()) - markerTable.append(HT.TR(markerTD)) - - marker_container.append(markerTable) - marker_div.append(marker_container) - - mapping_container.append(marker_div) - mapping_row.append(HT.TD(mapping_container)) - submitTable.append(mapping_row) - submitTable.append(mapping_script) - else: - submitTable.append(HT.TR(HT.TD(HT.Div(HT.Italic("mappingMethodId %s has not been implemented for this dataset yet." % mappingMethodId), id="mapping_tabs", Class="ui-tabs")))) - submitTable.append(mapping_script) - - else: - submitTable.append(HT.TR(HT.TD(HT.Div(HT.Italic("Mapping options are disabled for data not matched with genotypes."), id="mapping_tabs", Class="ui-tabs")))) - submitTable.append(mapping_script) - - title4Body.append(submitTable) - - - def natural_sort(strain_list): - - sorted = [] - for strain in strain_list: - try: - strain = int(strain) - try: sorted[-1] = sorted[-1] * 10 + strain - except: sorted.append(strain) - except: - sorted.append(strain) - return sorted - - ########################################## - ## Function to display trait tables - ########################################## - def dispTraitValues(self, fd , title5Body, varianceDataPage, nCols, mainForm, thisTrait): - traitTableOptions = HT.Div(style="border: 3px solid #EEEEEE; -moz-border-radius: 10px; -webkit-border-radius: 10px; width: 625px; padding: 5px 5px 10px 8px; font-size: 12px; background: #DDDDDD;") - resetButton = HT.Input(type='button',name='resetButton',value=' Reset ',Class="button") - blockSamplesField = HT.Input(type="text",style="background-color:white;border: 1px solid black;font-size: 14px;", name="removeField") - blockSamplesButton = HT.Input(type='button',value=' Block ', name='blockSamples', Class="button") - showHideNoValue = HT.Input(type='button', name='showHideNoValue', value=' Hide No Value ',Class='button') - blockMenuSpan = HT.Span(Id="blockMenuSpan") - blockMenu = HT.Select(name='block_method') - - if fd.genotype.type == "riset": - allstrainlist_neworder = fd.f1list + fd.strainlist - else: - allstrainlist_neworder = fd.f1list + fd.parlist + fd.strainlist - - attribute_ids = [] - attribute_names = [] - try: - #ZS: Id values for this trait's extra attributes; used to create "Exclude" dropdown and query for attribute values and create - self.cursor.execute("""SELECT CaseAttribute.Id, CaseAttribute.Name - FROM CaseAttribute, CaseAttributeXRef - WHERE CaseAttributeXRef.ProbeSetFreezeId = '%s' AND - CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId - group by CaseAttributeXRef.CaseAttributeId""" % (str(thisTrait.db.id))) - - exclude_menu = HT.Select(name="exclude_menu") - dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) - - for attribute in self.cursor.fetchall(): - attribute_ids.append(attribute[0]) - attribute_names.append(attribute[1]) - for this_attr_name in attribute_names: - exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) - self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value - FROM CaseAttribute, CaseAttributeXRef - WHERE CaseAttribute.Name = '%s' AND - CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""" % (this_attr_name)) - try: - distinct_values = self.cursor.fetchall() - attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus - attr_value_menu = HT.Select(name=this_attr_name) - attr_value_menu.append(("None", "show_all")) - for value in distinct_values: - attr_value_menu.append((str(value[0]), value[0])) - attr_value_menu_div.append(attr_value_menu) - dropdown_menus.append(attr_value_menu_div) - except: - pass - except: - pass - - other_strains = [] - for strain in thisTrait.data.keys(): - if strain not in allstrainlist_neworder: - other_strains.append(strain) - - if other_strains: - blockMenu.append(('%s Only' % fd.RISet,'1')) - blockMenu.append(('Non-%s Only' % fd.RISet,'0')) - blockMenuSpan.append(blockMenu) - else: - pass - - showHideOutliers = HT.Input(type='button', name='showHideOutliers', value=' Hide Outliers ', Class='button') - showHideMenuOptions = HT.Span(Id="showHideOptions", style="line-height:225%;") - if other_strains: - showHideMenuOptions.append(HT.Bold("  Block samples by index:    "), blockSamplesField, "   ", blockMenuSpan, "   ", blockSamplesButton, HT.BR()) - else: - showHideMenuOptions.append(HT.Bold("  Block samples by index:    "), blockSamplesField, "   ", blockSamplesButton, HT.BR()) - - exportButton = HT.Input(type='button', name='export', value=' Export ', Class='button') - if len(attribute_names) > 0: - excludeButton = HT.Input(type='button', name='excludeGroup', value=' Block ', Class='button') - showHideMenuOptions.append(HT.Bold("  Block samples by group:"), " "*5, exclude_menu, " "*5) - for menu in dropdown_menus: - showHideMenuOptions.append(menu) - showHideMenuOptions.append(" "*5, excludeButton, HT.BR()) - showHideMenuOptions.append(HT.Bold("  Options:"), " "*5, showHideNoValue, " "*5, showHideOutliers, " "*5, resetButton, " "*5, exportButton) - - traitTableOptions.append(showHideMenuOptions,HT.BR(),HT.BR()) - traitTableOptions.append(HT.Span("  Outliers highlighted in ", HT.Bold(" yellow ", style="background-color:yellow;"), " can be hidden using the ", - HT.Strong(" Hide Outliers "), " button,",HT.BR(),"  and samples with no value (x) can be hidden by clicking ", - HT.Strong(" Hide No Value "), "."), HT.BR()) - - - dispintro = HT.Paragraph("Edit or delete values in the Trait Data boxes, and use the ", HT.Strong("Reset"), " option as needed.",Class="fs12", style="margin-left:20px;") - - table = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target5") #Everything needs to be inside this table object in order for the toggle to work - container = HT.Div() #This will contain everything and be put into a cell of the table defined above - - container.append(dispintro, traitTableOptions, HT.BR()) - - primary_table = HT.TableLite(cellspacing=0, cellpadding=0, Id="sortable1", Class="tablesorter") - primary_header = self.getTableHeader(fd=fd, thisTrait=thisTrait, nCols=nCols, attribute_names=attribute_names) #Generate header for primary table object - - other_strainsExist = False - for strain in thisTrait.data.keys(): - if strain not in allstrainlist_neworder: - other_strainsExist = True - break - - primary_body = self.addTrait2Table(fd=fd, varianceDataPage=varianceDataPage, strainlist=allstrainlist_neworder, mainForm=mainForm, thisTrait=thisTrait, other_strainsExist=other_strainsExist, attribute_ids=attribute_ids, attribute_names=attribute_names, strains='primary') - - primary_table.append(primary_header) - for i in range(len(primary_body)): - primary_table.append(primary_body[i]) - - other_strains = [] - for strain in thisTrait.data.keys(): - if strain not in allstrainlist_neworder: - allstrainlist_neworder.append(strain) - other_strains.append(strain) - - if other_strains: - other_table = HT.TableLite(cellspacing=0, cellpadding=0, Id="sortable2", Class="tablesorter") #Table object with other (for example, non-BXD / MDP) traits - other_header = self.getTableHeader(fd=fd, thisTrait=thisTrait, nCols=nCols, attribute_names=attribute_names) #Generate header for other table object; same function is used as the one used for the primary table, since the header is the same - other_strains.sort() #Sort other strains - other_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_strains #Append F1 and parent strains to the beginning of the sorted list of other strains - - MDPText = HT.Span("Samples:", Class="ffl fwb fs12") - MDPMenu1 = HT.Select(name='MDPChoice1') - MDPMenu2 = HT.Select(name='MDPChoice2') - MDPMenu3 = HT.Select(name='MDPChoice3') - MDPMenu1.append(('%s Only' % fd.RISet,'1')) - MDPMenu2.append(('%s Only' % fd.RISet,'1')) - MDPMenu3.append(('%s Only' % fd.RISet,'1')) - MDPMenu1.append(('Non-%s Only' % fd.RISet,'2')) - MDPMenu2.append(('Non-%s Only' % fd.RISet,'2')) - MDPMenu3.append(('Non-%s Only' % fd.RISet,'2')) - MDPMenu1.append(('All Cases','0')) - MDPMenu2.append(('All Cases','0')) - MDPMenu3.append(('All Cases','0')) - self.MDPRow1.append(HT.TD(MDPText),HT.TD(MDPMenu1)) - self.MDPRow2.append(HT.TD(MDPText),HT.TD(MDPMenu2)) - self.MDPRow3.append(HT.TD(MDPText),HT.TD(MDPMenu3)) - - other_body = self.addTrait2Table(fd=fd, varianceDataPage=varianceDataPage, strainlist=other_strains, mainForm=mainForm, thisTrait=thisTrait, attribute_ids=attribute_ids, attribute_names=attribute_names, strains='other') - - other_table.append(other_header) - for i in range(len(other_body)): - other_table.append(other_body[i]) - else: - pass - - if other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) \ - or (fd.f1list and thisTrait.data.has_key(fd.f1list[1])): - fd.allstrainlist = allstrainlist_neworder - - if nCols == 6 and fd.varianceDispName != 'Variance': - mainForm.append(HT.Input(name='isSE', value="yes", type='hidden')) - - primary_div = HT.Div(primary_table, Id="primary") #Container for table with primary (for example, BXD) strain values - container.append(primary_div) - - if other_strains: - other_div = HT.Div(other_table, Id="other") #Container for table with other (for example, Non-BXD/MDP) strain values - container.append(HT.Div(' ', height=30)) - container.append(other_div) - - table.append(HT.TR(HT.TD(container))) - title5Body.append(table) - - def addTrait2Table(self, fd, varianceDataPage, strainlist, mainForm, thisTrait, other_strainsExist=None, attribute_ids=[], attribute_names=[], strains='primary'): - #XZ, Aug 23, 2010: I commented the code related to the display of animal case - #strainInfo = thisTrait.has_key('strainInfo') and thisTrait.strainInfo - - table_body = [] - vals = [] - - for i, strainNameOrig in enumerate(strainlist): - strainName = strainNameOrig.replace("_2nd_", "") - - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue - - vals.append(thisValFull) - - upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. - - for i, strainNameOrig in enumerate(strainlist): - - trId = strainNameOrig - selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)") - - strainName = strainNameOrig.replace("_2nd_", "") - strainNameAdd = '' - if fd.RISet == 'AXBXA' and strainName in ('AXB18/19/20','AXB13/14','BXA8/17'): - strainNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") - - try: - thisval, thisvar, thisNP = thisTrait.data[strainName].val, thisTrait.data[strainName].var, thisTrait.data[strainName].N - if thisNP: - mainForm.append(HT.Input(name='N'+strainName, value=thisNP, type='hidden')) - else: - pass - except: - thisval = thisvar = 'x' - - try: - traitVal = thisval - dispVal = "%2.3f" % thisval - except: - traitVal = '' - dispVal = 'x' - - strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl') - - if varianceDataPage: - try: - traitVar = thisvar - dispVar = "%2.3f" % thisvar - except: - traitVar = '' - dispVar = 'x' - - if thisval == 'x': - traitVar = '' #ZS: Used to be 0, but it doesn't seem like a good idea for values of 0 to *always* be at the bottom when you sort; it makes more sense to put "nothing" - - className = 'fs13 b1 c222 ' - valueClassName = 'fs13 b1 c222 valueField ' - rowClassName = 'novalue ' - else: - if (thisval >= upperBound) or (thisval <= lowerBound): - className = 'fs13 b1 c222 outlier ' - valueClassName = 'fs13 b1 c222 valueField ' - rowClassName = 'outlier' - else: - className = 'fs13 b1 c222 ' - valueClassName = 'fs13 b1 c222 valueField ' - rowClassName = ' ' - - if varianceDataPage: - varClassName = valueClassName + str(traitVar) - valueClassName += str(traitVal) - - if strainNameOrig == strainName: - if other_strainsExist and strainNameOrig in (fd.parlist + fd.f1list): - ######################################################################################################################################################## - # ZS: Append value and variance to the value and variance input fields' list of classes; this is so the javascript can update the value when the user - # changes it. The updated value is then used when the table is sorted (tablesorter.js). This needs to be done because the "value" attribute is immutable. - ######################################################################################################################################################### - - valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, - onChange= "javascript:this.form['_2nd_%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) - if varianceDataPage: - seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, - onChange= "javascript:this.form['V_2nd_%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) - else: - valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, Class=valueClassName) - if varianceDataPage: - seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, Class=varClassName) - else: - valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVal, - onChange= "javascript:this.form['%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) - if varianceDataPage: - seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, - onChange= "javascript:this.form['V%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) - - if (strains == 'primary'): - table_row = HT.TR(Id="Primary_"+str(i+1), Class=rowClassName) - else: - table_row = HT.TR(Id="Other_"+str(i+1), Class=rowClassName) - - if varianceDataPage: - table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) - table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) - table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) - table_row.append(HT.TD("±", width=20, align='center', Class=className)) - table_row.append(HT.TD(seField, width=80, align='right', Id="SE_"+str(i)+"_"+strains, Class=className)) - else: - table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) - table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) - table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) - - if thisTrait and thisTrait.db and thisTrait.db.type =='ProbeSet': - if len(attribute_ids) > 0: - - #ZS: Get StrainId value for the next query - self.cursor.execute("""SELECT Strain.Id - FROM Strain, StrainXRef, InbredSet - WHERE Strain.Name = '%s' and - StrainXRef.StrainId = Strain.Id and - InbredSet.Id = StrainXRef.InbredSetId and - InbredSet.Name = '%s'""" % (strainName, fd.RISet)) - - strain_id = self.cursor.fetchone()[0] - - attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column). - for attribute_id in attribute_ids: - - #ZS: Add extra case attribute values (if any) - self.cursor.execute("""SELECT Value - FROM CaseAttributeXRef - WHERE ProbeSetFreezeId = '%s' AND - StrainId = '%s' AND - CaseAttributeId = '%s' - group by CaseAttributeXRef.CaseAttributeId""" % (thisTrait.db.id, strain_id, str(attribute_id))) - - attributeValue = self.cursor.fetchone()[0] #Trait-specific attributes, if any - - #ZS: If it's an int, turn it into one for sorting (for example, 101 would be lower than 80 if they're strings instead of ints) - try: - attributeValue = int(attributeValue) - except: - pass - - span_Id = strains+"_attribute"+str(attr_counter)+"_sample"+str(i+1) - attr_container = HT.Span(attributeValue, Id=span_Id) - attr_className = str(attributeValue) + " " + className - table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) - attr_counter += 1 - - table_body.append(table_row) - return table_body - - def getTableHeader(self, fd, thisTrait, nCols, attribute_names): - - table_header = HT.TR() - - col_class = "fs13 fwb ff1 b1 cw cbrb" - - if nCols == 6: - try: - if fd.varianceDispName: - pass - except: - fd.varianceDispName = 'Variance' - - table_header.append(HT.TH('Index', align='right', width=60, Class=col_class), - HT.TH('Sample', align='right', width=100, Class=col_class), - HT.TH('Value', align='right', width=70, Class=col_class), - HT.TH(' ', width=20, Class=col_class), - HT.TH(fd.varianceDispName, align='right', width=80, Class=col_class)) - - elif nCols == 4: - table_header.append(HT.TH('Index', align='right', width=60, Class=col_class), - HT.TH('Sample', align='right', width=100, Class=col_class), - HT.TH('Value', align='right', width=70, Class=col_class)) - - else: - pass - - if len(attribute_names) > 0: - i=0 - for attribute in attribute_names: - char_count = len(attribute) - cell_width = char_count * 14 - table_header.append(HT.TH(attribute, align='right', width=cell_width, Class="attribute_name " + col_class)) - i+=1 - - return table_header - - - def getSortByValue(self): - - sortby = ("", "") - - return sortby + def __init__(self, fd, thisTrait=None): + + templatePage.__init__(self, fd) + + self.dict['title'] = 'Data Editing' + TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa") + + if not self.openMysql(): + return + if not fd.genotype: + fd.readData(incf1=1) + + ############################# + # determine data editing page format + ############################# + varianceDataPage = 0 + if fd.formID == 'varianceChoice': + varianceDataPage = 1 + + if varianceDataPage: + fmID='dataEditing' + nCols = 6 + else: + if fd.enablevariance: + fmID='pre_dataEditing' + nCols = 4 + else: + fmID='dataEditing' + nCols = 4 + + ############################# + ## titles, etc. + ############################# + + #titleTop = HT.Div() + # + #title1 = HT.Paragraph("  Details and Links", style="border-radius: 5px;", Id="title1", Class="sectionheader") + #title1Body = HT.Paragraph(Id="sectionbody1") + # + #if fd.enablevariance and not varianceDataPage: + # title2 = HT.Paragraph("  Submit Variance", style="border-radius: 5px;", Id="title2", Class="sectionheader") + #else: + # title2 = HT.Paragraph("  Basic Statistics", style="border-radius: 5px;", Id="title2", Class="sectionheader") + #title2Body = HT.Paragraph(Id="sectionbody2") + # + #title3 = HT.Paragraph("  Calculate Correlations", style="border-radius: 5px;", Id="title3", Class="sectionheader") + #title3Body = HT.Paragraph(Id="sectionbody3") + # + #title4 = HT.Paragraph("  Mapping Tools", style="border-radius: 5px;", Id="title4", Class="sectionheader") + #title4Body = HT.Paragraph(Id="sectionbody4") + # + #title5 = HT.Paragraph("  Review and Edit Data", style="border-radius: 5px;", Id="title5", Class="sectionheader") + #title5Body = HT.Paragraph(Id="sectionbody5") + + ############################# + ## Hidden field + ############################# + + # Some fields, like method, are defaulted to None; otherwise in IE the field can't be changed using jquery + hddn = { + 'FormID':fmID, + 'RISet':fd.RISet, + 'submitID':'', + 'scale':'physic', + 'additiveCheck':'ON', + 'showSNP':'ON', + 'showGenes':'ON', + 'method':None, + 'parentsf14regression':'OFF', + 'stats_method':'1', + 'chromosomes':'-1', + 'topten':'', + 'viewLegend':'ON', + 'intervalAnalystCheck':'ON', + 'valsHidden':'OFF', + 'database':'', + 'criteria':None, + 'MDPChoice':None, + 'bootCheck':None, + 'permCheck':None, + 'applyVarianceSE':None, + 'strainNames':'_', + 'strainVals':'_', + 'strainVars':'_', + 'otherStrainNames':'_', + 'otherStrainVals':'_', + 'otherStrainVars':'_', + 'extra_attributes':'_', + 'other_extra_attributes':'_' + } + + if fd.enablevariance: + hddn['enablevariance']='ON' + if fd.incparentsf1: + hddn['incparentsf1']='ON' + + if thisTrait: + hddn['fullname'] = str(thisTrait) + try: + hddn['normalPlotTitle'] = thisTrait.symbol + hddn['normalPlotTitle'] += ": " + hddn['normalPlotTitle'] += thisTrait.name + except: + hddn['normalPlotTitle'] = str(thisTrait.name) + hddn['fromDataEditingPage'] = 1 + if thisTrait.db and thisTrait.db.type and thisTrait.db.type == 'ProbeSet': + hddn['trait_type'] = thisTrait.db.type + if thisTrait.cellid: + hddn['cellid'] = thisTrait.cellid + else: + self.cursor.execute("SELECT h2 from ProbeSetXRef WHERE DataId = %d" % thisTrait.mysqlid) + heritability = self.cursor.fetchone() + hddn['heritability'] = heritability + + hddn['attribute_names'] = "" + + hddn['mappingMethodId'] = webqtlDatabaseFunction.getMappingMethod (cursor=self.cursor, groupName=fd.RISet) + + ############################# + ## Display Trait Information + ############################# + + #headSpan = self.dispHeader(fd,thisTrait) #Draw header + # + #titleTop.append(headSpan) + + if fd.identification: + hddn['identification'] = fd.identification + + else: + hddn['identification'] = "Un-named trait" #If no identification, set identification to un-named + + self.dispTraitInformation(fd, "", hddn, thisTrait) #Display trait information + function buttons + + ############################# + ## Generate form and buttons + ############################# + + mainForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), + name='dataInput', submit=HT.Input(type='hidden')) + + next=HT.Input(type='submit', name='submit',value='Next',Class="button") + reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button") + correlationMenus = [] + + if thisTrait == None: + thisTrait = webqtlTrait(data=fd.allTraitData, db=None) + + # Variance submit page only + if fd.enablevariance and not varianceDataPage: + title2Body.append("Click the next button to go to the variance submission form.", + HT.Center(next,reset)) + else: + self.dispBasicStatistics(fd, title2Body, thisTrait) + self.dispCorrelationTools(fd, title3Body, thisTrait) + self.dispMappingTools(fd, title4Body, thisTrait) + + ############################# + ## Trait Value Table + ############################# + + self.dispTraitValues(fd, title5Body, varianceDataPage, nCols, mainForm, thisTrait) + + if fd.allstrainlist: + hddn['allstrainlist'] = string.join(fd.allstrainlist, ' ') + for key in hddn.keys(): + mainForm.append(HT.Input(name=key, value=hddn[key], type='hidden')) + + if fd.enablevariance and not varianceDataPage: + #pre dataediting page, need to submit variance + mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body) + else: + mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body) + TD_LR.append(HT.Paragraph(mainForm)) + self.dict['body'] = str(TD_LR) + + ########################################## + ## Function to display header + ########################################## + def dispHeader(self, fd, thisTrait): + headSpan = HT.Div(style="font-size:14px;") + + #If trait, use trait name; otherwise, use identification value + if thisTrait: + if thisTrait.cellid: + headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Probe ID ', thisTrait.cellid) + else: + headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Record ID ', thisTrait.name) + else: + if fd.identification: + headSpan.append(HT.Strong('Trait ID ', style='font-size:16px;'),fd.identification) + else: + headSpan.append(HT.Strong('Un-named Trait', style='font-size:16px;')) + + return headSpan + + ########################################## + ## Function to display trait infos + ########################################## + def dispTraitInformation(self, fd, title1Body, hddn, thisTrait): + + _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) + + #tbl = HT.TableLite(cellpadding=2, Class="collap", style="margin-left:20px;", width="840", valign="top", id="target1") + + #reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button") + + #XZ, August 02, 2011: The display of icons is decided by the trait type (if trait exists), along with user log-in status. Note that the new submitted trait might not be trait object. + addSelectionButton = "" + verifyButton = "" + rnaseqButton = "" + geneWikiButton = "" + probeButton = "" + similarButton = "" + snpBrowserButton = "" + updateButton = "" + + addSelectionText = "" + verifyText = "" + rnaseqText = "" + geneWikiText = "" + probeText = "" + similarText = "" + snpBrowserText = "" + updateText = "" + + if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']: + + if thisTrait==None or thisTrait.db.type=='Temp': + updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'addPublish');") + updateButton_img = HT.Image("/images/edit_icon.jpg", name="addnew", alt="Add To Publish", title="Add To Publish", style="border:none;") + updateButton.append(updateButton_img) + updateText = "Edit" + elif thisTrait.db.type != 'Temp': + if thisTrait.db.type == 'Publish' and thisTrait.confidential: #XZ: confidential phenotype trait + if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users): + updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") + updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") + updateButton.append(updateButton_img) + updateText = "Edit" + else: + updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") + updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") + updateButton.append(updateButton_img) + updateText = "Edit" + else: + pass + + self.cursor.execute('SELECT Name FROM InbredSet WHERE Name="%s"' % fd.RISet) + if thisTrait: + addSelectionButton = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (fd.RISet, 'dataInput')) + addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;") + #addSelectionButton.append(addSelectionButton_img) + addSelectionText = "Add" + elif self.cursor.fetchall(): + addSelectionButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('%s')[0], 'addRecord');" % ('dataInput')) + addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="", alt="Add To Collection", title="Add To Collection", style="border:none;") + #addSelectionButton.append(addSelectionButton_img) + addSelectionText = "Add" + else: + pass + + + # Microarray database information to display + if thisTrait and thisTrait.db and thisTrait.db.type == 'ProbeSet': #before, this line was only reached if thisTrait != 0, but now we need to check + try: + hddn['GeneId'] = int(string.strip(thisTrait.geneid)) + except: + pass + + #Info2Disp = HT.Paragraph() + + #XZ: Gene Symbol + if thisTrait.symbol: + #XZ: Show SNP Browser only for mouse + if _Species == 'mouse': + self.cursor.execute("select geneSymbol from GeneList where geneSymbol = %s", thisTrait.symbol) + geneName = self.cursor.fetchone() + if geneName: + snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + "&geneName=%s" % geneName[0] + else: + if thisTrait.chr and thisTrait.mb: + snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + \ + "&chr=%s&start=%2.6f&end=%2.6f" % (thisTrait.chr, thisTrait.mb-0.002, thisTrait.mb+0.002) + else: + snpurl = "" + + if snpurl: + snpBrowserButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % snpurl) + snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="snpbrowser", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;") + snpBrowserButton.append(snpBrowserButton_img) + snpBrowserText = "SNPs" + + #XZ: Show GeneWiki for all species + geneWikiButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + "?FormID=geneWiki&symbol=%s" % thisTrait.symbol)) + geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="genewiki", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;") + geneWikiButton.append(geneWikiButton_img) + geneWikiText = 'GeneWiki' + + #XZ: display similar traits in other selected datasets + if thisTrait and thisTrait.db and thisTrait.db.type=="ProbeSet" and thisTrait.symbol: + if _Species in ("mouse", "rat", "human"): + similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.symbol, _Species) + similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl) + similarButton_img = HT.Image("/images/find_icon.jpg", name="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;") + similarButton.append(similarButton_img) + similarText = "Find" + else: + pass + tbl.append(HT.TR( + HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span('%s' % thisTrait.symbol, valign="top", Class="fs13 fsI"), valign="top", width=740) + )) + else: + tbl.append(HT.TR( + HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span('Not available', Class="fs13 fsI"), valign="top") + )) + + #XZ: Gene Alias + if thisTrait.alias: + alias = string.replace(thisTrait.alias, ";", " ") + alias = string.join(string.split(alias), ", ") + tbl.append(HT.TR( + HT.TD('Aliases: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(alias, Class="fs13 fsI"), valign="top") + )) + + #XZ: Description + if thisTrait.description: + tSpan = HT.Span(thisTrait.description, Class="fs13") + if thisTrait.probe_target_description: + tSpan.append('; ', thisTrait.probe_target_description) + else: + tSpan = HT.Span('Not available', Class="fs13") + tbl.append(HT.TR( + HT.TD('Description: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top") + )) + + #XZ: Location + + #XZ: deal with Chr and Mb + if thisTrait.chr and thisTrait.mb: + tSpan = HT.Span('Chr %s @ %s Mb' % (thisTrait.chr,thisTrait.mb),Class="fs13") + elif (thisTrait.chr): + tSpan = HT.Span('Chr %s @ Unknown position' % (thisTrait.chr), Class="fs13") + else: + tSpan = HT.Span('Not available', Class="fs13") + + #XZ: deal with direction + if thisTrait.strand_probe == '+': + tSpan.append(' on the plus strand ') + elif thisTrait.strand_probe == '-': + tSpan.append(' on the minus strand ') + else: + pass + + tbl.append(HT.TR( + HT.TD('Location: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top") + )) + + ##display Verify Location button + try: + blatsequence = thisTrait.blatseq + if not blatsequence: + #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. + self.cursor.execute("""SELECT Probe.Sequence, Probe.Name + FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetFreeze.Name = '%s' AND + ProbeSet.Name = '%s' AND + Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (thisTrait.db.name, thisTrait.name) ) + seqs = self.cursor.fetchall() + if not seqs: + raise ValueError + else: + blatsequence = '' + for seqt in seqs: + if int(seqt[1][-1]) % 2 == 1: + blatsequence += string.strip(seqt[0]) + + #--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe + blatsequence = '%3E'+thisTrait.name+'%0A'+blatsequence+'%0A' + #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. + self.cursor.execute("""SELECT Probe.Sequence, Probe.Name + FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetFreeze.Name = '%s' AND + ProbeSet.Name = '%s' AND + Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (thisTrait.db.name, thisTrait.name) ) + + seqs = self.cursor.fetchall() + for seqt in seqs: + if int(seqt[1][-1]) %2 == 1: + blatsequence += '%3EProbe_'+string.strip(seqt[1])+'%0A'+string.strip(seqt[0])+'%0A' + #-------- + #XZ, 07/16/2009: targetsequence is not used, so I comment out this block + #targetsequence = thisTrait.targetseq + #if targetsequence==None: + # targetsequence = "" + + #XZ: Pay attention to the parameter of version (rn, mm, hg). They need to be changed if necessary. + if _Species == "rat": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence) + UTHSC_BLAT_URL = "" + elif _Species == "mouse": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence) + UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', blatsequence) + elif _Species == "human": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) + UTHSC_BLAT_URL = "" + else: + UCSC_BLAT_URL = "" + UTHSC_BLAT_URL = "" + + if UCSC_BLAT_URL: + verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL) + verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", + title=" Check probe locations at UCSC ", style="border:none;") + verifyButton.append(verifyButtonImg) + verifyText = 'Verify' + if UTHSC_BLAT_URL: + rnaseqButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UTHSC_BLAT_URL) + rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", + title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") + rnaseqButton.append(rnaseqButtonImg) + rnaseqText = 'RNA-seq' + tSpan.append(HT.BR()) + except: + pass + + #Display probe information (if any) + if thisTrait.db.name.find('Liver') >= 0 and thisTrait.db.name.find('F2') < 0: + pass + else: + #query database for number of probes associated with trait; if count > 0, set probe tool button and text + self.cursor.execute("""SELECT count(*) + FROM Probe, ProbeSet + WHERE ProbeSet.Name = '%s' AND Probe.ProbeSetId = ProbeSet.Id""" % (thisTrait.name)) + + probeResult = self.cursor.fetchone() + if probeResult[0] > 0: + probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&RISet=%s&incparentsf1=ON" \ + % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.db, thisTrait.name, thisTrait.cellid, fd.RISet) + probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl) + probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;") + probeButton.append(probeButton_img) + probeText = "Probes" + + tSpan = HT.Span(Class="fs13") + + #XZ: deal with blat score and blat specificity. + if thisTrait.probe_set_specificity or thisTrait.probe_set_blat_score: + if thisTrait.probe_set_specificity: + tSpan.append(HT.Href(url="/blatInfo.html", target="_blank", title="Values higher than 2 for the specificity are good", text="BLAT specificity", Class="non_bold"),": %.1f" % float(thisTrait.probe_set_specificity), " "*3) + if thisTrait.probe_set_blat_score: + tSpan.append("Score: %s" % int(thisTrait.probe_set_blat_score), " "*2) + + onClick="openNewWin('/blatInfo.html')" + + tbl.append(HT.TR( + HT.TD('Target Score: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top") + )) + + tSpan = HT.Span(Class="fs13") + tSpan.append(str(_Species).capitalize(), ", ", fd.RISet) + + tbl.append(HT.TR( + HT.TD('Species and Group: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top") + )) + + if thisTrait.cellid: + self.cursor.execute(""" + select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze + where + ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND + ProbeSetFreeze.Id = %d""" % thisTrait.db.id) + probeDBName = self.cursor.fetchone()[0] + tbl.append(HT.TR( + HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span('%s' % probeDBName, Class="non_bold"), valign="top") + )) + else: + tbl.append(HT.TR( + HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name, + target='_blank', Class="fs13 fwn non_bold"), valign="top") + )) + + #XZ: ID links + if thisTrait.genbankid or thisTrait.geneid or thisTrait.unigeneid or thisTrait.omim or thisTrait.homologeneid: + idStyle = "background:#dddddd;padding:2" + tSpan = HT.Span(Class="fs13") + if thisTrait.geneid: + gurl = HT.Href(text= 'Gene', target='_blank',\ + url=webqtlConfig.NCBI_LOCUSID % thisTrait.geneid, Class="fs14 fwn", title="Info from NCBI Entrez Gene") + tSpan.append(HT.Span(gurl, style=idStyle), " "*2) + if thisTrait.omim: + gurl = HT.Href(text= 'OMIM', target='_blank', \ + url= webqtlConfig.OMIM_ID % thisTrait.omim,Class="fs14 fwn", title="Summary from On Mendelian Inheritance in Man") + tSpan.append(HT.Span(gurl, style=idStyle), " "*2) + if thisTrait.unigeneid: + try: + gurl = HT.Href(text= 'UniGene',target='_blank',\ + url= webqtlConfig.UNIGEN_ID % tuple(string.split(thisTrait.unigeneid,'.')[:2]),Class="fs14 fwn", title="UniGene ID") + tSpan.append(HT.Span(gurl, style=idStyle), " "*2) + except: + pass + if thisTrait.genbankid: + thisTrait.genbankid = '|'.join(thisTrait.genbankid.split('|')[0:10]) + if thisTrait.genbankid[-1]=='|': + thisTrait.genbankid=thisTrait.genbankid[0:-1] + gurl = HT.Href(text= 'GenBank', target='_blank', \ + url= webqtlConfig.GENBANK_ID % thisTrait.genbankid,Class="fs14 fwn", title="Find the original GenBank sequence used to design the probes") + tSpan.append(HT.Span(gurl, style=idStyle), " "*2) + if thisTrait.homologeneid: + hurl = HT.Href(text= 'HomoloGene', target='_blank',\ + url=webqtlConfig.HOMOLOGENE_ID % thisTrait.homologeneid, Class="fs14 fwn", title="Find similar genes in other species") + tSpan.append(HT.Span(hurl, style=idStyle), " "*2) + + tbl.append( + HT.TR(HT.TD(colspan=3,height=6)), + HT.TR( + HT.TD('Resource Links: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top") + )) + + #XZ: Resource Links: + if thisTrait.symbol: + linkStyle = "background:#dddddd;padding:2" + tSpan = HT.Span(style="font-family:verdana,serif;font-size:13px") + + #XZ,12/26/2008: Gene symbol may contain single quotation mark. + #For example, Affymetrix, mouse430v2, 1440338_at, the symbol is 2'-Pde (geneid 211948) + #I debug this by using double quotation marks. + if _Species == "rat": + + #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more + #symatlas_species = "Rattus norvegicus" + + #self.cursor.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = '%s'" % thisTrait.symbol) + self.cursor.execute('SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = "%s"' % thisTrait.symbol) + try: + kgId, chr, txst, txen = self.cursor.fetchall()[0] + if chr and txst and txen and kgId: + txst = int(txst*1000000) + txen = int(txen*1000000) + tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\ + title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('rn3',kgId,chr,txst,txen),Class="fs14 fwn"), style=linkStyle) + , " "*2) + except: + pass + if _Species == "mouse": + + #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more + #symatlas_species = "Mus musculus" + + #self.cursor.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = '%s'" % thisTrait.symbol) + self.cursor.execute('SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = "%s"' % thisTrait.symbol) + try: + chr, txst, txen = self.cursor.fetchall()[0] + if chr and txst and txen and thisTrait.refseq_transcriptid : + txst = int(txst*1000000) + txen = int(txen*1000000) + tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\ + title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('mm9',thisTrait.refseq_transcriptid,chr,txst,txen), + Class="fs14 fwn"), style=linkStyle) + , " "*2) + except: + pass + + #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more + #tSpan.append(HT.Span(HT.Href(text= 'SymAtlas',target="mainFrame",\ + # url="http://symatlas.gnf.org/SymAtlas/bioentry?querytext=%s&query=14&species=%s&type=Expression" \ + # % (thisTrait.symbol,symatlas_species),Class="fs14 fwn", \ + # title="Expression across many tissues and cell types"), style=linkStyle), " "*2) + if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"): + tSpan.append(HT.Span(HT.Href(text= 'BioGPS',target="mainFrame",\ + url="http://biogps.gnf.org/?org=%s#goto=genereport&id=%s" \ + % (_Species, thisTrait.geneid),Class="fs14 fwn", \ + title="Expression across many tissues and cell types"), style=linkStyle), " "*2) + tSpan.append(HT.Span(HT.Href(text= 'STRING',target="mainFrame",\ + url="http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=%s" \ + % thisTrait.symbol,Class="fs14 fwn", \ + title="Protein interactions: known and inferred"), style=linkStyle), " "*2) + if thisTrait.symbol: + #ZS: The "species scientific" converts the plain English species names we're using to their scientific names, which are needed for PANTHER's input + #We should probably use the scientific name along with the English name (if not instead of) elsewhere as well, given potential non-English speaking users + if _Species == "mouse": + species_scientific = "Mus%20musculus" + elif _Species == "rat": + species_scientific = "Rattus%20norvegicus" + elif _Species == "human": + species_scientific = "Homo%20sapiens" + elif _Species == "drosophila": + species_scientific = "Drosophila%20melanogaster" + else: + species_scientific = "all" + + species_scientific + tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \ + url="http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=%s&listType=1&fieldValue=%s" \ + % (species_scientific, thisTrait.symbol),Class="fs14 fwn", \ + title="Gene and protein data resources from Celera-ABI"), style=linkStyle), " "*2) + else: + pass + #tSpan.append(HT.Span(HT.Href(text= 'BIND',target="mainFrame",\ + # url="http://bind.ca/?textquery=%s" \ + # % thisTrait.symbol,Class="fs14 fwn", \ + # title="Protein interactions"), style=linkStyle), " "*2) + if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"): + tSpan.append(HT.Span(HT.Href(text= 'Gemma',target="mainFrame",\ + url="http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" \ + % thisTrait.geneid, Class="fs14 fwn", \ + title="Meta-analysis of gene expression data"), style=linkStyle), " "*2) + tSpan.append(HT.Span(HT.Href(text= 'SynDB',target="mainFrame",\ + url="http://lily.uthsc.edu:8080/20091027_GNInterfaces/20091027_redirectSynDB.jsp?query=%s" \ + % thisTrait.symbol, Class="fs14 fwn", \ + title="Brain synapse database"), style=linkStyle), " "*2) + if _Species == "mouse": + tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ + url="http://mouse.brain-map.org/brain/%s.html" \ + % thisTrait.symbol, Class="fs14 fwn", \ + title="Allen Brain Atlas"), style=linkStyle), " "*2) + + if thisTrait.geneid: + #if _Species == "mouse": + # tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ + # url="http://www.brain-map.org/search.do?queryText=egeneid=%s" \ + # % thisTrait.geneid, Class="fs14 fwn", \ + # title="Allen Brain Atlas"), style=linkStyle), " "*2) + if _Species == "human": + tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ + url="http://humancortex.alleninstitute.org/has/human/imageseries/search/1.html?searchSym=t&searchAlt=t&searchName=t&gene_term=&entrez_term=%s" \ + % thisTrait.geneid, Class="fs14 fwn", \ + title="Allen Brain Atlas"), style=linkStyle), " "*2) + tbl.append( + HT.TR(HT.TD(colspan=3,height=6)), + HT.TR( + HT.TD(' '), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top"))) + + menuTable = HT.TableLite(cellpadding=2, Class="collap", width="620", id="target1") + menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(similarButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(geneWikiButton, align="center"),HT.TD(snpBrowserButton, align="center"),HT.TD(rnaseqButton, align="center"),HT.TD(probeButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(similarText, align="center"),HT.TD(verifyText, align="center"),HT.TD(geneWikiText, align="center"),HT.TD(snpBrowserText, align="center"),HT.TD(rnaseqText, align="center"),HT.TD(probeText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + + + #for zhou mi's cliques, need to be removed + #if self.database[:6] == 'BXDMic' and self.ProbeSetID in cliqueID: + # Info2Disp.append(HT.Strong('Clique Search: '),HT.Href(text='Search',\ + # url ="http://compbio1.utmem.edu/clique_go/results.php?pid=%s&pval_1=0&pval_2=0.001" \ + # % self.ProbeSetID,target='_blank',Class="normalsize"),HT.BR()) + + #linkTable.append(HT.TR(linkTD)) + #Info2Disp.append(linkTable) + title1Body.append(tbl, HT.BR(), menuTable) + + elif thisTrait and thisTrait.db and thisTrait.db.type =='Publish': #Check if trait is phenotype + + if thisTrait.confidential: + tbl.append(HT.TR( + HT.TD('Pre-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.pre_publication_description, Class="fs13"), valign="top", width=740) + )) + if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users): + tbl.append(HT.TR( + HT.TD('Post-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Pre-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.pre_publication_abbreviation, Class="fs13"), valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Post-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.post_publication_abbreviation, Class="fs13"), valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Lab code: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.lab_code, Class="fs13"), valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Owner: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.owner, Class="fs13"), valign="top", width=740) + )) + else: + tbl.append(HT.TR( + HT.TD('Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Authors: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.authors, Class="fs13"), + valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Title: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.title, Class="fs13"), + valign="top", width=740) + )) + if thisTrait.journal: + journal = thisTrait.journal + if thisTrait.year: + journal = thisTrait.journal + " (%s)" % thisTrait.year + + tbl.append(HT.TR( + HT.TD('Journal: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(journal, Class="fs13"), + valign="top", width=740) + )) + PubMedLink = "" + if thisTrait.pubmed_id: + PubMedLink = webqtlConfig.PUBMEDLINK_URL % thisTrait.pubmed_id + if PubMedLink: + tbl.append(HT.TR( + HT.TD('Link: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(HT.Href(url=PubMedLink, text="PubMed",target='_blank',Class="fs14 fwn"), + style = "background:#cddcff;padding:2"), valign="top", width=740) + )) + + menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1") + menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + + title1Body.append(tbl, HT.BR(), menuTable) + + elif thisTrait and thisTrait.db and thisTrait.db.type == 'Geno': #Check if trait is genotype + + GenoInfo = HT.Paragraph() + if thisTrait.chr and thisTrait.mb: + location = ' Chr %s @ %s Mb' % (thisTrait.chr,thisTrait.mb) + else: + location = "not available" + + if thisTrait.sequence and len(thisTrait.sequence) > 100: + if _Species == "rat": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', thisTrait.sequence) + UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('rat', 'rn3', thisTrait.sequence) + elif _Species == "mouse": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', thisTrait.sequence) + UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', thisTrait.sequence) + elif _Species == "human": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) + UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('human', 'hg19', thisTrait.sequence) + else: + UCSC_BLAT_URL = "" + UTHSC_BLAT_URL = "" + if UCSC_BLAT_URL: + #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL) + verifyButton = HT.Href(url="#") + verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;") + verifyButton.append(verifyButtonImg) + verifyText = "Verify" + rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL) + rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") + rnaseqButton.append(rnaseqButtonImg) + rnaseqText = "RNA-seq" + + tbl.append(HT.TR( + HT.TD('Location: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(location, Class="fs13"), valign="top", width=740) + ), + HT.TR( + HT.TD('SNP Search: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp&cmd=search&term=%s" % thisTrait.name, 'NCBI',Class="fs13"), + valign="top", width=740) + )) + + menuTable = HT.TableLite(cellpadding=2, Class="collap", width="275", id="target1") + menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(rnaseqButton, align="center"), HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(verifyText, align="center"),HT.TD(rnaseqText, align="center"), HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + + title1Body.append(tbl, HT.BR(), menuTable) + + elif (thisTrait == None or thisTrait.db.type == 'Temp'): #if temporary trait (user-submitted trait or PCA trait) + + TempInfo = HT.Paragraph() + if thisTrait != None: + if thisTrait.description: + tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),' %s ' % thisTrait.description,HT.BR()), colspan=3, height=15)) + else: + tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),'not available',HT.BR(),HT.BR()), colspan=3, height=15)) + + if (updateText == "Edit"): + menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1") + else: + menuTable = HT.TableLite(cellpadding=2, Class="collap", width="80", id="target1") + + menuTable.append(HT.TR(HT.TD(addSelectionButton, align="right"),HT.TD(updateButton, align="right"), colspan=3, height=50, style="vertical-align:bottom;") ) + menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + + title1Body.append(tbl, HT.BR(), menuTable) + + else: + pass + + + ########################################## + ## Function to display analysis tools + ########################################## + def dispBasicStatistics(self, fd, title2Body, thisTrait): + + #XZ, June 22, 2011: The definition and usage of primary_strains, other_strains, specialStrains, all_strains are not clear and hard to understand. But since they are only used in this function for draw graph purpose, they will not hurt the business logic outside. As of June 21, 2011, this function seems work fine, so no hurry to clean up. These parameters and code in this function should be cleaned along with fd.f1list, fd.parlist, fd.strainlist later. + stats_row = HT.TR() + stats_cell = HT.TD() + + if fd.genotype.type == "riset": + strainlist = fd.f1list + fd.strainlist + else: + strainlist = fd.f1list + fd.parlist + fd.strainlist + + other_strains = [] #XZ: strain that is not of primary group + specialStrains = [] #XZ: This might be replaced by other_strains / ZS: It is just other strains without parent/f1 strains. + all_strains = [] + primary_strains = [] #XZ: strain of primary group, e.g., BXD, LXS + + MDP_menu = HT.Select(name='stats_mdp', Class='stats_mdp') + + for strain in thisTrait.data.keys(): + strainName = strain.replace("_2nd_", "") + if strain not in strainlist: + if (thisTrait.data[strainName].val != None): + if strain.find('F1') < 0: + specialStrains.append(strain) + if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)): + other_strains.append(strain) #XZ: at current stage, other_strains doesn't include parent strains and F1 strains of primary group + else: + if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)): + primary_strains.append(strain) #XZ: at current stage, the primary_strains is the same as fd.strainlist / ZS: I tried defining primary_strains as fd.strainlist instead, but in some cases it ended up including the parent strains (1436869_at BXD) + + if len(other_strains) > 3: + other_strains.sort(key=webqtlUtil.natsort_key) + primary_strains.sort(key=webqtlUtil.natsort_key) + primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains #XZ: note that fd.f1list and fd.parlist are added. + all_strains = primary_strains + other_strains + other_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_strains #XZ: note that fd.f1list and fd.parlist are added. + MDP_menu.append(('All Cases','0')) + MDP_menu.append(('%s Only' % fd.RISet,'1')) + MDP_menu.append(('Non-%s Only' % fd.RISet,'2')) + stats_row.append("Include: ", MDP_menu, HT.BR(), HT.BR()) + else: + if (len(other_strains) > 0) and (len(primary_strains) + len(other_strains) > 3): + MDP_menu.append(('All Cases','0')) + MDP_menu.append(('%s Only' % fd.RISet,'1')) + MDP_menu.append(('Non-%s Only' % fd.RISet,'2')) + stats_row.append("Include: ", MDP_menu, " "*3) + all_strains = primary_strains + all_strains.sort(key=webqtlUtil.natsort_key) + all_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + all_strains + primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains + else: + all_strains = strainlist + + other_strains.sort(key=webqtlUtil.natsort_key) + all_strains = all_strains + other_strains + pass + + update_button = HT.Input(type='button',value=' Update Figures ', Class="button update") #This is used to reload the page and update the Basic Statistics figures with user-edited data + stats_row.append(update_button, HT.BR(), HT.BR()) + + if (len(other_strains)) > 0 and (len(primary_strains) + len(other_strains) > 4): + #One set of vals for all, selected strain only, and non-selected only + vals1 = [] + vals2 = [] + vals3 = [] + + #Using all strains/cases for values + for i, strainNameOrig in enumerate(all_strains): + strainName = strainNameOrig.replace("_2nd_", "") + + try: + thisval = thisTrait.data[strainName].val + thisvar = thisTrait.data[strainName].var + thisValFull = [strainName,thisval,thisvar] + except: + continue + + vals1.append(thisValFull) + + #Using just the RISet strain + for i, strainNameOrig in enumerate(primary_strains): + strainName = strainNameOrig.replace("_2nd_", "") + + try: + thisval = thisTrait.data[strainName].val + thisvar = thisTrait.data[strainName].var + thisValFull = [strainName,thisval,thisvar] + except: + continue + + vals2.append(thisValFull) + + #Using all non-RISet strains only + for i, strainNameOrig in enumerate(other_strains): + strainName = strainNameOrig.replace("_2nd_", "") + + try: + thisval = thisTrait.data[strainName].val + thisvar = thisTrait.data[strainName].var + thisValFull = [strainName,thisval,thisvar] + except: + continue + + vals3.append(thisValFull) + + vals_set = [vals1,vals2,vals3] + + else: + vals = [] + + #Using all strains/cases for values + for i, strainNameOrig in enumerate(all_strains): + strainName = strainNameOrig.replace("_2nd_", "") + + try: + thisval = thisTrait.data[strainName].val + thisvar = thisTrait.data[strainName].var + thisValFull = [strainName,thisval,thisvar] + except: + continue + + vals.append(thisValFull) + + vals_set = [vals] + + stats_script = HT.Script(language="Javascript") #script needed for tabs + + for i, vals in enumerate(vals_set): + if i == 0 and len(vals) < 4: + stats_container = HT.Div(id="stats_tabs", style="padding:10px;", Class="ui-tabs") #Needed for tabs; notice the "stats_script_text" below referring to this element + stats_container.append(HT.Div(HT.Italic("Fewer than 4 case data were entered. No statistical analysis has been attempted."))) + stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" + stats_cell.append(stats_container) + break + elif (i == 1 and len(primary_strains) < 4): + stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") + stats_container.append(HT.Div(HT.Italic("Fewer than 4 " + fd.RISet + " case data were entered. No statistical analysis has been attempted."))) + elif (i == 2 and len(other_strains) < 4): + stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") + stats_container.append(HT.Div(HT.Italic("Fewer than 4 non-" + fd.RISet + " case data were entered. No statistical analysis has been attempted."))) + stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});""" + else: + stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") + stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});""" + if len(vals) > 4: + stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-5", Class="stats_tab"), + HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"), + HT.Href(text="Box Plot", url="#statstabs-2", Class="stats_tab")] + stats_tabs = HT.List(stats_tab_list) + stats_container.append(stats_tabs) + + table_div = HT.Div(id="statstabs-1") + table_container = HT.Paragraph() + + statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + + if thisTrait.db: + if thisTrait.cellid: + statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=thisTrait.db.type, cellid=thisTrait.cellid) + else: + statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=thisTrait.db.type) + else: + statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals) + + statsTable.append(HT.TR(HT.TD(statsTableCell))) + + table_container.append(statsTable) + table_div.append(table_container) + stats_container.append(table_div) + + normalplot_div = HT.Div(id="statstabs-5") + normalplot_container = HT.Paragraph() + normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + + try: + plotTitle = thisTrait.symbol + plotTitle += ": " + plotTitle += thisTrait.name + except: + plotTitle = str(thisTrait.name) + + normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains) + normalplot.append(HT.TR(HT.TD(normalplot_img))) + normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \ + normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(), + "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", + target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary")))) + normalplot_container.append(normalplot) + normalplot_div.append(normalplot_container) + stats_container.append(normalplot_div) + + boxplot_div = HT.Div(id="statstabs-2") + boxplot_container = HT.Paragraph() + boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals) + boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left"))) + boxplot_container.append(boxplot) + boxplot_div.append(boxplot_container) + stats_container.append(boxplot_div) + + + barName_div = HT.Div(id="statstabs-3") + barName_container = HT.Paragraph() + barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name") + barName.append(HT.TR(HT.TD(barName_img))) + barName_container.append(barName) + barName_div.append(barName_container) + stats_container.append(barName_div) + + barRank_div = HT.Div(id="statstabs-4") + barRank_container = HT.Paragraph() + barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank") + barRank.append(HT.TR(HT.TD(barRank_img))) + barRank_container.append(barRank) + barRank_div.append(barRank_container) + stats_container.append(barRank_div) + + stats_cell.append(stats_container) + + stats_script.append(stats_script_text) + + submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") + stats_row.append(stats_cell) + + submitTable.append(stats_row) + submitTable.append(stats_script) + + title2Body.append(submitTable) + + + def dispCorrelationTools(self, fd, title3Body, thisTrait): + + _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) + + RISetgp = fd.RISet + if RISetgp[:3] == 'BXD': + RISetgp = 'BXD' + + if RISetgp: + sample_correlation = HT.Input(type='button',name='sample_corr', value=' Compute ', Class="button sample_corr") + lit_correlation = HT.Input(type='button',name='lit_corr', value=' Compute ', Class="button lit_corr") + tissue_correlation = HT.Input(type='button',name='tiss_corr', value=' Compute ', Class="button tiss_corr") + methodText = HT.Span("Calculate:", Class="ffl fwb fs12") + + databaseText = HT.Span("Database:", Class="ffl fwb fs12") + databaseMenu1 = HT.Select(name='database1') + databaseMenu2 = HT.Select(name='database2') + databaseMenu3 = HT.Select(name='database3') + + nmenu = 0 + self.cursor.execute('SELECT PublishFreeze.FullName,PublishFreeze.Name FROM \ + PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id \ + and InbredSet.Name = "%s" and PublishFreeze.public > %d' % \ + (RISetgp,webqtlConfig.PUBLICTHRESH)) + for item in self.cursor.fetchall(): + databaseMenu1.append(item) + databaseMenu2.append(item) + databaseMenu3.append(item) + nmenu += 1 + self.cursor.execute('SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze,\ + InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = \ + "%s" and GenoFreeze.public > %d' % (RISetgp,webqtlConfig.PUBLICTHRESH)) + for item in self.cursor.fetchall(): + databaseMenu1.append(item) + databaseMenu2.append(item) + databaseMenu3.append(item) + nmenu += 1 + #03/09/2009: Xiaodong changed the SQL query to order by Name as requested by Rob. + self.cursor.execute('SELECT Id, Name FROM Tissue order by Name') + for item in self.cursor.fetchall(): + TId, TName = item + databaseMenuSub = HT.Optgroup(label = '%s ------' % TName) + self.cursor.execute('SELECT ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze, \ + InbredSet WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = %d and \ + ProbeSetFreeze.public > %d and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like "%s%%" \ + order by ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId ' % (TId,webqtlConfig.PUBLICTHRESH, RISetgp)) + for item2 in self.cursor.fetchall(): + databaseMenuSub.append(item2) + nmenu += 1 + databaseMenu1.append(databaseMenuSub) + databaseMenu2.append(databaseMenuSub) + databaseMenu3.append(databaseMenuSub) + if nmenu: + if thisTrait and thisTrait.db != None: + databaseMenu1.selected.append(thisTrait.db.fullname) + databaseMenu2.selected.append(thisTrait.db.fullname) + databaseMenu3.selected.append(thisTrait.db.fullname) + + criteriaText = HT.Span("Return:", Class="ffl fwb fs12") + + criteriaMenu1 = HT.Select(name='criteria1', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") + criteriaMenu1.append(('top 100','100')) + criteriaMenu1.append(('top 200','200')) + criteriaMenu1.append(('top 500','500')) + criteriaMenu1.append(('top 1000','1000')) + criteriaMenu1.append(('top 2000','2000')) + criteriaMenu1.append(('top 5000','5000')) + criteriaMenu1.append(('top 10000','10000')) + criteriaMenu1.append(('top 15000','15000')) + criteriaMenu1.append(('top 20000','20000')) + + criteriaMenu2 = HT.Select(name='criteria2', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") + criteriaMenu2.append(('top 100','100')) + criteriaMenu2.append(('top 200','200')) + criteriaMenu2.append(('top 500','500')) + criteriaMenu2.append(('top 1000','1000')) + criteriaMenu2.append(('top 2000','2000')) + criteriaMenu2.append(('top 5000','5000')) + criteriaMenu2.append(('top 10000','10000')) + criteriaMenu2.append(('top 15000','15000')) + criteriaMenu2.append(('top 20000','20000')) + + criteriaMenu3 = HT.Select(name='criteria3', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") + criteriaMenu3.append(('top 100','100')) + criteriaMenu3.append(('top 200','200')) + criteriaMenu3.append(('top 500','500')) + criteriaMenu3.append(('top 1000','1000')) + criteriaMenu3.append(('top 2000','2000')) + criteriaMenu3.append(('top 5000','5000')) + criteriaMenu3.append(('top 10000','10000')) + criteriaMenu3.append(('top 15000','15000')) + criteriaMenu3.append(('top 20000','20000')) + + + self.MDPRow1 = HT.TR(Class='mdp1') + self.MDPRow2 = HT.TR(Class='mdp2') + self.MDPRow3 = HT.TR(Class='mdp3') + + correlationMenus1 = HT.TableLite( + HT.TR(HT.TD(databaseText), HT.TD(databaseMenu1, colspan="3")), + HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu1)), + self.MDPRow1, cellspacing=0, width="619px", cellpadding=2) + correlationMenus1.append(HT.Input(name='orderBy', value='2', type='hidden')) # to replace the orderBy menu + correlationMenus2 = HT.TableLite( + HT.TR(HT.TD(databaseText), HT.TD(databaseMenu2, colspan="3")), + HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu2)), + self.MDPRow2, cellspacing=0, width="619px", cellpadding=2) + correlationMenus2.append(HT.Input(name='orderBy', value='2', type='hidden')) + correlationMenus3 = HT.TableLite( + HT.TR(HT.TD(databaseText), HT.TD(databaseMenu3, colspan="3")), + HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu3)), + self.MDPRow3, cellspacing=0, width="619px", cellpadding=2) + correlationMenus3.append(HT.Input(name='orderBy', value='2', type='hidden')) + + else: + correlationMenus = "" + + + corr_row = HT.TR() + corr_container = HT.Div(id="corr_tabs", Class="ui-tabs") + + if (thisTrait.db != None and thisTrait.db.type =='ProbeSet'): + corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1"), HT.Href(text='Literature r', url="#corrtabs-2"), HT.Href(text='Tissue r', url="#corrtabs-3")] + else: + corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1")] + + corr_tabs = HT.List(corr_tab_list) + corr_container.append(corr_tabs) + + if correlationMenus1 or correlationMenus2 or correlationMenus3: + sample_div = HT.Div(id="corrtabs-1") + sample_container = HT.Span() + + sample_type = HT.Input(type="radio", name="sample_method", value="1", checked="checked") + sample_type2 = HT.Input(type="radio", name="sample_method", value="2") + + sampleTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + sampleTD = HT.TD(correlationMenus1, HT.BR(), + "Pearson", sample_type, " "*3, "Spearman Rank", sample_type2, HT.BR(), HT.BR(), + sample_correlation, HT.BR(), HT.BR()) + + sampleTD.append(HT.Span("The ",HT.Href(url="/correlationAnnotation.html#sample_r", target="_blank", text="Sample Correlation")," is computed between trait data and", + " any ",HT.BR()," other traits in the sample database selected above. Use ", + HT.Href(url="/glossary.html#Correlations", target="_blank", text="Spearman Rank"), + HT.BR(),"when the sample size is small (<20) or when there are influential \ + outliers.", HT.BR(),Class="fs12")) + + sampleTable.append(sampleTD) + + sample_container.append(sampleTable) + sample_div.append(sample_container) + corr_container.append(sample_div) + + literature_div = HT.Div(id="corrtabs-2") + literature_container = HT.Span() + + literatureTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + literatureTD = HT.TD(correlationMenus2,HT.BR(),lit_correlation, HT.BR(), HT.BR()) + literatureTD.append(HT.Span("The ", HT.Href(url="/correlationAnnotation.html", target="_blank",text="Literature Correlation"), " (Lit r) between this gene and all other genes is computed",HT.BR(), + "using the ", HT.Href(url="https://grits.eecs.utk.edu/sgo/sgo.html", target="_blank", text="Semantic Gene Organizer"), + " and human, rat, and mouse data from PubMed. ", HT.BR(),"Values are ranked by Lit r, \ + but Sample r and Tissue r are also displayed.", HT.BR(), HT.BR(), + HT.Href(url="/glossary.html#Literature", target="_blank", text="More on using Lit r"), Class="fs12")) + literatureTable.append(literatureTD) + + literature_container.append(literatureTable) + literature_div.append(literature_container) + + if thisTrait.db != None: + if (thisTrait.db.type =='ProbeSet'): + corr_container.append(literature_div) + + tissue_div = HT.Div(id="corrtabs-3") + tissue_container = HT.Span() + + tissue_type = HT.Input(type="radio", name="tissue_method", value="4", checked="checked") + tissue_type2 = HT.Input(type="radio", name="tissue_method", value="5") + + tissueTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + tissueTD = HT.TD(correlationMenus3,HT.BR(), + "Pearson", tissue_type, " "*3, "Spearman Rank", tissue_type2, HT.BR(), HT.BR(), + tissue_correlation, HT.BR(), HT.BR()) + tissueTD.append(HT.Span("The ", HT.Href(url="/webqtl/main.py?FormID=tissueCorrelation", target="_blank", text="Tissue Correlation"), + " (Tissue r) estimates the similarity of expression of two genes",HT.BR()," or \ + transcripts across different cells, tissues, or organs (",HT.Href(url="/correlationAnnotation.html#tissue_r", target="_blank", text="glossary"),"). \ + Tissue correlations",HT.BR()," are generated by analyzing expression in multiple samples usually taken from \ + single cases.",HT.BR(),HT.Bold("Pearson")," and ",HT.Bold("Spearman Rank")," correlations have been computed for all pairs \ + of genes",HT.BR()," using data from mouse samples.", + HT.BR(), Class="fs12")) + tissueTable.append(tissueTD) + + tissue_container.append(tissueTable) + tissue_div.append(tissue_container) + if thisTrait.db != None: + if (thisTrait.db.type =='ProbeSet'): + corr_container.append(tissue_div) + + corr_row.append(HT.TD(corr_container)) + + corr_script = HT.Script(language="Javascript") + corr_script_text = """$(function() { $("#corr_tabs").tabs(); });""" + corr_script.append(corr_script_text) + + submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target4") + submitTable.append(corr_row) + submitTable.append(corr_script) + + title3Body.append(submitTable) + + + def dispMappingTools(self, fd, title4Body, thisTrait): + + _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) + + RISetgp = fd.RISet + if RISetgp[:3] == 'BXD': + RISetgp = 'BXD' + + #check boxes - one for regular interval mapping, the other for composite + permCheck1= HT.Input(type='checkbox', Class='checkbox', name='permCheck1',checked="on") + bootCheck1= HT.Input(type='checkbox', Class='checkbox', name='bootCheck1',checked=0) + permCheck2= HT.Input(type='checkbox', Class='checkbox', name='permCheck2',checked="on") + bootCheck2= HT.Input(type='checkbox', Class='checkbox', name='bootCheck2',checked=0) + optionbox1 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression1',checked=0) + optionbox2 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression2',checked=0) + optionbox3 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression3',checked=0) + applyVariance1 = HT.Input(name='applyVarianceSE1',type='checkbox', Class='checkbox') + applyVariance2 = HT.Input(name='applyVarianceSE2',type='checkbox', Class='checkbox') + + IntervalMappingButton=HT.Input(type='button' ,name='interval',value=' Compute ', Class="button") + CompositeMappingButton=HT.Input(type='button' ,name='composite',value=' Compute ', Class="button") + MarkerRegressionButton=HT.Input(type='button',name='marker', value=' Compute ', Class="button") + + chrText = HT.Span("Chromosome:", Class="ffl fwb fs12") + + # updated by NL 5-28-2010 + # Interval Mapping + chrMenu = HT.Select(name='chromosomes1') + chrMenu.append(tuple(["All",-1])) + for i in range(len(fd.genotype)): + if len(fd.genotype[i]) > 1: + chrMenu.append(tuple([fd.genotype[i].name,i])) + + #Menu for Composite Interval Mapping + chrMenu2 = HT.Select(name='chromosomes2') + chrMenu2.append(tuple(["All",-1])) + for i in range(len(fd.genotype)): + if len(fd.genotype[i]) > 1: + chrMenu2.append(tuple([fd.genotype[i].name,i])) + + if fd.genotype.Mbmap: + scaleText = HT.Span("Mapping Scale:", Class="ffl fwb fs12") + scaleMenu1 = HT.Select(name='scale1', onChange="checkUncheck(window.document.dataInput.scale1.value, window.document.dataInput.permCheck1, window.document.dataInput.bootCheck1)") + scaleMenu1.append(("Megabase",'physic')) + scaleMenu1.append(("Centimorgan",'morgan')) + scaleMenu2 = HT.Select(name='scale2', onChange="checkUncheck(window.document.dataInput.scale2.value, window.document.dataInput.permCheck2, window.document.dataInput.bootCheck2)") + scaleMenu2.append(("Megabase",'physic')) + scaleMenu2.append(("Centimorgan",'morgan')) + + controlText = HT.Span("Control Locus:", Class="ffl fwb fs12") + controlMenu = HT.Input(type="text", name="controlLocus", Class="controlLocus") + + if fd.genotype.Mbmap: + intMappingMenu = HT.TableLite( + HT.TR(HT.TD(chrText), HT.TD(chrMenu, colspan="3")), + HT.TR(HT.TD(scaleText), HT.TD(scaleMenu1)), + cellspacing=0, width="263px", cellpadding=2) + compMappingMenu = HT.TableLite( + HT.TR(HT.TD(chrText), HT.TD(chrMenu2, colspan="3")), + HT.TR(HT.TD(scaleText), HT.TD(scaleMenu2)), + HT.TR(HT.TD(controlText), HT.TD(controlMenu)), + cellspacing=0, width="325px", cellpadding=2) + else: + intMappingMenu = HT.TableLite( + HT.TR(HT.TD(chrText), HT.TD(chrMenu, colspan="3")), + cellspacing=0, width="263px", cellpadding=2) + compMappingMenu = HT.TableLite( + HT.TR(HT.TD(chrText), HT.TD(chrMenu2, colspan="3")), + HT.TR(HT.TD(controlText), HT.TD(controlMenu)), + cellspacing=0, width="325px", cellpadding=2) + + directPlotButton = "" + directPlotButton = HT.Input(type='button',name='', value=' Compute ',\ + onClick="dataEditingFunc(this.form,'directPlot');",Class="button") + directPlotSortText = HT.Span(HT.Bold("Sort by: "), Class="ffl fwb fs12") + directPlotSortMenu = HT.Select(name='graphSort') + directPlotSortMenu.append(('LRS Full',0)) + directPlotSortMenu.append(('LRS Interact',1)) + directPlotPermuText = HT.Span("Permutation Test (n=500)", Class="ffl fs12") + directPlotPermu = HT.Input(type='checkbox', Class='checkbox',name='directPermuCheckbox', checked="on") + pairScanReturnText = HT.Span(HT.Bold("Return: "), Class="ffl fwb fs12") + pairScanReturnMenu = HT.Select(name='pairScanReturn') + pairScanReturnMenu.append(('top 50','50')) + pairScanReturnMenu.append(('top 100','100')) + pairScanReturnMenu.append(('top 200','200')) + pairScanReturnMenu.append(('top 500','500')) + + pairScanMenus = HT.TableLite( + HT.TR(HT.TD(directPlotSortText), HT.TD(directPlotSortMenu)), + HT.TR(HT.TD(pairScanReturnText), HT.TD(pairScanReturnMenu)), + cellspacing=0, width="232px", cellpadding=2) + + markerSuggestiveText = HT.Span(HT.Bold("Display LRS greater than:"), Class="ffl fwb fs12") + markerSuggestive = HT.Input(name='suggestive', size=5, maxlength=8) + displayAllText = HT.Span(" Display all LRS ", Class="ffl fs12") + displayAll = HT.Input(name='displayAllLRS', type="checkbox", Class='checkbox') + useParentsText = HT.Span(" Use Parents ", Class="ffl fs12") + useParents = optionbox2 + applyVarianceText = HT.Span(" Use Weighted ", Class="ffl fs12") + + markerMenu = HT.TableLite( + HT.TR(HT.TD(markerSuggestiveText), HT.TD(markerSuggestive)), + HT.TR(HT.TD(displayAll,displayAllText)), + HT.TR(HT.TD(useParents,useParentsText)), + HT.TR(HT.TD(applyVariance2,applyVarianceText)), + cellspacing=0, width="263px", cellpadding=2) + + + mapping_row = HT.TR() + mapping_container = HT.Div(id="mapping_tabs", Class="ui-tabs") + + mapping_tab_list = [HT.Href(text="Interval", url="#mappingtabs-1"), HT.Href(text="Marker Regression", url="#mappingtabs-2"), HT.Href(text="Composite", url="#mappingtabs-3"), HT.Href(text="Pair-Scan", url="#mappingtabs-4")] + mapping_tabs = HT.List(mapping_tab_list) + mapping_container.append(mapping_tabs) + + interval_div = HT.Div(id="mappingtabs-1") + interval_container = HT.Span() + + intervalTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + intTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") + intTD.append(intMappingMenu,HT.BR()) + + intTD.append(permCheck1,'Permutation Test (n=2000)',HT.BR(), + bootCheck1,'Bootstrap Test (n=2000)', HT.BR(), optionbox1, 'Use Parents', HT.BR(), + applyVariance1,'Use Weighted', HT.BR(), HT.BR(),IntervalMappingButton, HT.BR(), HT.BR()) + intervalTable.append(HT.TR(intTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#intmap', target='_blank', text='Interval Mapping'), + ' computes linkage maps for the entire genome or single',HT.BR(),' chromosomes.', + ' The ',HT.Href(url='/glossary.html#permutation', target='_blank', text='Permutation Test'),' estimates suggestive and significant ',HT.BR(),' linkage scores. \ + The ',HT.Href(url='/glossary.html#bootstrap', target='_blank', text='Bootstrap Test'), ' estimates the precision of the QTL location.' + ,Class="fs12"), HT.BR(), valign="top"))) + + interval_container.append(intervalTable) + interval_div.append(interval_container) + mapping_container.append(interval_div) + + # Marker Regression + + marker_div = HT.Div(id="mappingtabs-2") + marker_container = HT.Span() + + markerTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + markerTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") + markerTD.append(markerMenu,HT.BR()) + + markerTD.append(MarkerRegressionButton,HT.BR(),HT.BR()) + + markerTable.append(HT.TR(markerTD),HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#',target='_blank',text='Marker regression'), + ' computes and displays LRS values for individual markers.',HT.BR(), + 'This function also lists additive effects (phenotype units per allele) and', HT.BR(), + 'dominance deviations for some datasets.', HT.BR(),Class="fs12"), HT.BR(), valign="top"))) + + marker_container.append(markerTable) + marker_div.append(marker_container) + mapping_container.append(marker_div) + + # Composite interval mapping + composite_div = HT.Div(id="mappingtabs-3") + composite_container = HT.Span() + + compositeTable = HT.TableLite(cellspacing=0, cellpadding=3, width="100%") + compTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") + compTD.append(compMappingMenu,HT.BR()) + + compTD.append(permCheck2, 'Permutation Test (n=2000)',HT.BR(), + bootCheck2,'Bootstrap Test (n=2000)', HT.BR(), + optionbox3, 'Use Parents', HT.BR(), HT.BR(), CompositeMappingButton, HT.BR(), HT.BR()) + compositeTable.append(HT.TR(compTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#Composite',target='_blank',text='Composite Interval Mapping'), + " allows you to control for a single marker as",HT.BR()," a cofactor. ", + "To find a control marker, run the ",HT.Bold("Marker Regression")," function."), + HT.BR(), valign="top"))) + + composite_container.append(compositeTable) + composite_div.append(composite_container) + mapping_container.append(composite_div) + + # Pair Scan + + pairscan_div = HT.Div(id="mappingtabs-4") + pairscan_container = HT.Span() + + pairScanTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + pairScanTD = HT.TD(NOWRAP='ON', Class="fs12 fwn") + pairScanTD.append(pairScanMenus,HT.BR()) + pairScanTD.append(directPlotPermu, directPlotPermuText, HT.BR(), HT.BR(), + directPlotButton,HT.BR(),HT.BR()) + pairScanTable.append(HT.TR(pairScanTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#Pair_Scan', target="_blank", text='Pair-Scan'), + ' searches for pairs of chromosomal regions that are',HT.BR(), + 'involved in two-locus epistatic interactions.'), HT.BR(), valign="top"))) + + pairscan_container.append(pairScanTable) + pairscan_div.append(pairscan_container) + mapping_container.append(pairscan_div) + + mapping_row.append(HT.TD(mapping_container)) + + # Treat Interval Mapping and Marker Regression and Pair Scan as a group for displaying + #disable Interval Mapping and Marker Regression and Pair Scan for human and the dataset doesn't have genotype file + mappingMethodId = webqtlDatabaseFunction.getMappingMethod(cursor=self.cursor, groupName=RISetgp) + + mapping_script = HT.Script(language="Javascript") + mapping_script_text = """$(function() { $("#mapping_tabs").tabs(); });""" + mapping_script.append(mapping_script_text) + + submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") + + if mappingMethodId != None: + if int(mappingMethodId) == 1: + submitTable.append(mapping_row) + submitTable.append(mapping_script) + elif int(mappingMethodId) == 4: + # NL; 09-26-2011 testing for Human Genome Association function + mapping_row=HT.TR() + mapping_container = HT.Div(id="mapping_tabs", Class="ui-tabs") + + mapping_tab_list = [HT.Href(text="Genome Association", url="#mappingtabs-1")] + mapping_tabs = HT.List(mapping_tab_list) + mapping_container.append(mapping_tabs) + + # Genome Association + markerSuggestiveText = HT.Span(HT.Bold("P Value:"), Class="ffl fwb fs12") + + markerSuggestive = HT.Input(name='pValue', value='0.001', size=10, maxlength=20,onClick="this.value='';",onBlur="if(this.value==''){this.value='0.001'};") + markerMenu = HT.TableLite(HT.TR(HT.TD(markerSuggestiveText), HT.TD(markerSuggestive),HT.TD(HT.Italic('   (e.g. 0.001 or 1e-3 or 1E-3 or 3)'))),cellspacing=0, width="400px", cellpadding=2) + MarkerRegressionButton=HT.Input(type='button',name='computePlink', value='  Compute Using PLINK  ', onClick= "validatePvalue(this.form);", Class="button") + + marker_div = HT.Div(id="mappingtabs-1") + marker_container = HT.Span() + markerTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + markerTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") + markerTD.append(markerMenu,HT.BR()) + markerTD.append(MarkerRegressionButton,HT.BR(),HT.BR()) + markerTable.append(HT.TR(markerTD)) + + marker_container.append(markerTable) + marker_div.append(marker_container) + + mapping_container.append(marker_div) + mapping_row.append(HT.TD(mapping_container)) + submitTable.append(mapping_row) + submitTable.append(mapping_script) + else: + submitTable.append(HT.TR(HT.TD(HT.Div(HT.Italic("mappingMethodId %s has not been implemented for this dataset yet." % mappingMethodId), id="mapping_tabs", Class="ui-tabs")))) + submitTable.append(mapping_script) + + else: + submitTable.append(HT.TR(HT.TD(HT.Div(HT.Italic("Mapping options are disabled for data not matched with genotypes."), id="mapping_tabs", Class="ui-tabs")))) + submitTable.append(mapping_script) + + title4Body.append(submitTable) + + + def natural_sort(strain_list): + + sorted = [] + for strain in strain_list: + try: + strain = int(strain) + try: sorted[-1] = sorted[-1] * 10 + strain + except: sorted.append(strain) + except: + sorted.append(strain) + return sorted + + ########################################## + ## Function to display trait tables + ########################################## + def dispTraitValues(self, fd , title5Body, varianceDataPage, nCols, mainForm, thisTrait): + traitTableOptions = HT.Div(style="border: 3px solid #EEEEEE; -moz-border-radius: 10px; -webkit-border-radius: 10px; width: 625px; padding: 5px 5px 10px 8px; font-size: 12px; background: #DDDDDD;") + resetButton = HT.Input(type='button',name='resetButton',value=' Reset ',Class="button") + blockSamplesField = HT.Input(type="text",style="background-color:white;border: 1px solid black;font-size: 14px;", name="removeField") + blockSamplesButton = HT.Input(type='button',value=' Block ', name='blockSamples', Class="button") + showHideNoValue = HT.Input(type='button', name='showHideNoValue', value=' Hide No Value ',Class='button') + blockMenuSpan = HT.Span(Id="blockMenuSpan") + blockMenu = HT.Select(name='block_method') + + if fd.genotype.type == "riset": + allstrainlist_neworder = fd.f1list + fd.strainlist + else: + allstrainlist_neworder = fd.f1list + fd.parlist + fd.strainlist + + attribute_ids = [] + attribute_names = [] + try: + #ZS: Id values for this trait's extra attributes; used to create "Exclude" dropdown and query for attribute values and create + self.cursor.execute("""SELECT CaseAttribute.Id, CaseAttribute.Name + FROM CaseAttribute, CaseAttributeXRef + WHERE CaseAttributeXRef.ProbeSetFreezeId = '%s' AND + CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId + group by CaseAttributeXRef.CaseAttributeId""" % (str(thisTrait.db.id))) + + exclude_menu = HT.Select(name="exclude_menu") + dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) + + for attribute in self.cursor.fetchall(): + attribute_ids.append(attribute[0]) + attribute_names.append(attribute[1]) + for this_attr_name in attribute_names: + exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) + self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value + FROM CaseAttribute, CaseAttributeXRef + WHERE CaseAttribute.Name = '%s' AND + CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""" % (this_attr_name)) + try: + distinct_values = self.cursor.fetchall() + attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus + attr_value_menu = HT.Select(name=this_attr_name) + attr_value_menu.append(("None", "show_all")) + for value in distinct_values: + attr_value_menu.append((str(value[0]), value[0])) + attr_value_menu_div.append(attr_value_menu) + dropdown_menus.append(attr_value_menu_div) + except: + pass + except: + pass + + other_strains = [] + for strain in thisTrait.data.keys(): + if strain not in allstrainlist_neworder: + other_strains.append(strain) + + if other_strains: + blockMenu.append(('%s Only' % fd.RISet,'1')) + blockMenu.append(('Non-%s Only' % fd.RISet,'0')) + blockMenuSpan.append(blockMenu) + else: + pass + + showHideOutliers = HT.Input(type='button', name='showHideOutliers', value=' Hide Outliers ', Class='button') + showHideMenuOptions = HT.Span(Id="showHideOptions", style="line-height:225%;") + if other_strains: + showHideMenuOptions.append(HT.Bold("  Block samples by index:    "), blockSamplesField, "   ", blockMenuSpan, "   ", blockSamplesButton, HT.BR()) + else: + showHideMenuOptions.append(HT.Bold("  Block samples by index:    "), blockSamplesField, "   ", blockSamplesButton, HT.BR()) + + exportButton = HT.Input(type='button', name='export', value=' Export ', Class='button') + if len(attribute_names) > 0: + excludeButton = HT.Input(type='button', name='excludeGroup', value=' Block ', Class='button') + showHideMenuOptions.append(HT.Bold("  Block samples by group:"), " "*5, exclude_menu, " "*5) + for menu in dropdown_menus: + showHideMenuOptions.append(menu) + showHideMenuOptions.append(" "*5, excludeButton, HT.BR()) + showHideMenuOptions.append(HT.Bold("  Options:"), " "*5, showHideNoValue, " "*5, showHideOutliers, " "*5, resetButton, " "*5, exportButton) + + traitTableOptions.append(showHideMenuOptions,HT.BR(),HT.BR()) + traitTableOptions.append(HT.Span("  Outliers highlighted in ", HT.Bold(" yellow ", style="background-color:yellow;"), " can be hidden using the ", + HT.Strong(" Hide Outliers "), " button,",HT.BR(),"  and samples with no value (x) can be hidden by clicking ", + HT.Strong(" Hide No Value "), "."), HT.BR()) + + + dispintro = HT.Paragraph("Edit or delete values in the Trait Data boxes, and use the ", HT.Strong("Reset"), " option as needed.",Class="fs12", style="margin-left:20px;") + + table = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target5") #Everything needs to be inside this table object in order for the toggle to work + container = HT.Div() #This will contain everything and be put into a cell of the table defined above + + container.append(dispintro, traitTableOptions, HT.BR()) + + primary_table = HT.TableLite(cellspacing=0, cellpadding=0, Id="sortable1", Class="tablesorter") + primary_header = self.getTableHeader(fd=fd, thisTrait=thisTrait, nCols=nCols, attribute_names=attribute_names) #Generate header for primary table object + + other_strainsExist = False + for strain in thisTrait.data.keys(): + if strain not in allstrainlist_neworder: + other_strainsExist = True + break + + primary_body = self.addTrait2Table(fd=fd, varianceDataPage=varianceDataPage, strainlist=allstrainlist_neworder, mainForm=mainForm, thisTrait=thisTrait, other_strainsExist=other_strainsExist, attribute_ids=attribute_ids, attribute_names=attribute_names, strains='primary') + + primary_table.append(primary_header) + for i in range(len(primary_body)): + primary_table.append(primary_body[i]) + + other_strains = [] + for strain in thisTrait.data.keys(): + if strain not in allstrainlist_neworder: + allstrainlist_neworder.append(strain) + other_strains.append(strain) + + if other_strains: + other_table = HT.TableLite(cellspacing=0, cellpadding=0, Id="sortable2", Class="tablesorter") #Table object with other (for example, non-BXD / MDP) traits + other_header = self.getTableHeader(fd=fd, thisTrait=thisTrait, nCols=nCols, attribute_names=attribute_names) #Generate header for other table object; same function is used as the one used for the primary table, since the header is the same + other_strains.sort() #Sort other strains + other_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_strains #Append F1 and parent strains to the beginning of the sorted list of other strains + + MDPText = HT.Span("Samples:", Class="ffl fwb fs12") + MDPMenu1 = HT.Select(name='MDPChoice1') + MDPMenu2 = HT.Select(name='MDPChoice2') + MDPMenu3 = HT.Select(name='MDPChoice3') + MDPMenu1.append(('%s Only' % fd.RISet,'1')) + MDPMenu2.append(('%s Only' % fd.RISet,'1')) + MDPMenu3.append(('%s Only' % fd.RISet,'1')) + MDPMenu1.append(('Non-%s Only' % fd.RISet,'2')) + MDPMenu2.append(('Non-%s Only' % fd.RISet,'2')) + MDPMenu3.append(('Non-%s Only' % fd.RISet,'2')) + MDPMenu1.append(('All Cases','0')) + MDPMenu2.append(('All Cases','0')) + MDPMenu3.append(('All Cases','0')) + self.MDPRow1.append(HT.TD(MDPText),HT.TD(MDPMenu1)) + self.MDPRow2.append(HT.TD(MDPText),HT.TD(MDPMenu2)) + self.MDPRow3.append(HT.TD(MDPText),HT.TD(MDPMenu3)) + + other_body = self.addTrait2Table(fd=fd, varianceDataPage=varianceDataPage, strainlist=other_strains, mainForm=mainForm, thisTrait=thisTrait, attribute_ids=attribute_ids, attribute_names=attribute_names, strains='other') + + other_table.append(other_header) + for i in range(len(other_body)): + other_table.append(other_body[i]) + else: + pass + + if other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) \ + or (fd.f1list and thisTrait.data.has_key(fd.f1list[1])): + fd.allstrainlist = allstrainlist_neworder + + if nCols == 6 and fd.varianceDispName != 'Variance': + mainForm.append(HT.Input(name='isSE', value="yes", type='hidden')) + + primary_div = HT.Div(primary_table, Id="primary") #Container for table with primary (for example, BXD) strain values + container.append(primary_div) + + if other_strains: + other_div = HT.Div(other_table, Id="other") #Container for table with other (for example, Non-BXD/MDP) strain values + container.append(HT.Div(' ', height=30)) + container.append(other_div) + + table.append(HT.TR(HT.TD(container))) + title5Body.append(table) + + def addTrait2Table(self, fd, varianceDataPage, strainlist, mainForm, thisTrait, other_strainsExist=None, attribute_ids=[], attribute_names=[], strains='primary'): + #XZ, Aug 23, 2010: I commented the code related to the display of animal case + #strainInfo = thisTrait.has_key('strainInfo') and thisTrait.strainInfo + + table_body = [] + vals = [] + + for i, strainNameOrig in enumerate(strainlist): + strainName = strainNameOrig.replace("_2nd_", "") + + try: + thisval = thisTrait.data[strainName].val + thisvar = thisTrait.data[strainName].var + thisValFull = [strainName,thisval,thisvar] + except: + continue + + vals.append(thisValFull) + + upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. + + for i, strainNameOrig in enumerate(strainlist): + + trId = strainNameOrig + selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)") + + strainName = strainNameOrig.replace("_2nd_", "") + strainNameAdd = '' + if fd.RISet == 'AXBXA' and strainName in ('AXB18/19/20','AXB13/14','BXA8/17'): + strainNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") + + try: + thisval, thisvar, thisNP = thisTrait.data[strainName].val, thisTrait.data[strainName].var, thisTrait.data[strainName].N + if thisNP: + mainForm.append(HT.Input(name='N'+strainName, value=thisNP, type='hidden')) + else: + pass + except: + thisval = thisvar = 'x' + + try: + traitVal = thisval + dispVal = "%2.3f" % thisval + except: + traitVal = '' + dispVal = 'x' + + strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl') + + if varianceDataPage: + try: + traitVar = thisvar + dispVar = "%2.3f" % thisvar + except: + traitVar = '' + dispVar = 'x' + + if thisval == 'x': + traitVar = '' #ZS: Used to be 0, but it doesn't seem like a good idea for values of 0 to *always* be at the bottom when you sort; it makes more sense to put "nothing" + + className = 'fs13 b1 c222 ' + valueClassName = 'fs13 b1 c222 valueField ' + rowClassName = 'novalue ' + else: + if (thisval >= upperBound) or (thisval <= lowerBound): + className = 'fs13 b1 c222 outlier ' + valueClassName = 'fs13 b1 c222 valueField ' + rowClassName = 'outlier' + else: + className = 'fs13 b1 c222 ' + valueClassName = 'fs13 b1 c222 valueField ' + rowClassName = ' ' + + if varianceDataPage: + varClassName = valueClassName + str(traitVar) + valueClassName += str(traitVal) + + if strainNameOrig == strainName: + if other_strainsExist and strainNameOrig in (fd.parlist + fd.f1list): + ######################################################################################################################################################## + # ZS: Append value and variance to the value and variance input fields' list of classes; this is so the javascript can update the value when the user + # changes it. The updated value is then used when the table is sorted (tablesorter.js). This needs to be done because the "value" attribute is immutable. + ######################################################################################################################################################### + + valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, + onChange= "javascript:this.form['_2nd_%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) + if varianceDataPage: + seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, + onChange= "javascript:this.form['V_2nd_%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) + else: + valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, Class=valueClassName) + if varianceDataPage: + seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, Class=varClassName) + else: + valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVal, + onChange= "javascript:this.form['%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) + if varianceDataPage: + seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, + onChange= "javascript:this.form['V%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) + + if (strains == 'primary'): + table_row = HT.TR(Id="Primary_"+str(i+1), Class=rowClassName) + else: + table_row = HT.TR(Id="Other_"+str(i+1), Class=rowClassName) + + if varianceDataPage: + table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) + table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) + table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) + table_row.append(HT.TD("±", width=20, align='center', Class=className)) + table_row.append(HT.TD(seField, width=80, align='right', Id="SE_"+str(i)+"_"+strains, Class=className)) + else: + table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) + table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) + table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) + + if thisTrait and thisTrait.db and thisTrait.db.type =='ProbeSet': + if len(attribute_ids) > 0: + + #ZS: Get StrainId value for the next query + self.cursor.execute("""SELECT Strain.Id + FROM Strain, StrainXRef, InbredSet + WHERE Strain.Name = '%s' and + StrainXRef.StrainId = Strain.Id and + InbredSet.Id = StrainXRef.InbredSetId and + InbredSet.Name = '%s'""" % (strainName, fd.RISet)) + + strain_id = self.cursor.fetchone()[0] + + attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column). + for attribute_id in attribute_ids: + + #ZS: Add extra case attribute values (if any) + self.cursor.execute("""SELECT Value + FROM CaseAttributeXRef + WHERE ProbeSetFreezeId = '%s' AND + StrainId = '%s' AND + CaseAttributeId = '%s' + group by CaseAttributeXRef.CaseAttributeId""" % (thisTrait.db.id, strain_id, str(attribute_id))) + + attributeValue = self.cursor.fetchone()[0] #Trait-specific attributes, if any + + #ZS: If it's an int, turn it into one for sorting (for example, 101 would be lower than 80 if they're strings instead of ints) + try: + attributeValue = int(attributeValue) + except: + pass + + span_Id = strains+"_attribute"+str(attr_counter)+"_sample"+str(i+1) + attr_container = HT.Span(attributeValue, Id=span_Id) + attr_className = str(attributeValue) + " " + className + table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) + attr_counter += 1 + + table_body.append(table_row) + return table_body + + def getTableHeader(self, fd, thisTrait, nCols, attribute_names): + + table_header = HT.TR() + + col_class = "fs13 fwb ff1 b1 cw cbrb" + + if nCols == 6: + try: + if fd.varianceDispName: + pass + except: + fd.varianceDispName = 'Variance' + + table_header.append(HT.TH('Index', align='right', width=60, Class=col_class), + HT.TH('Sample', align='right', width=100, Class=col_class), + HT.TH('Value', align='right', width=70, Class=col_class), + HT.TH(' ', width=20, Class=col_class), + HT.TH(fd.varianceDispName, align='right', width=80, Class=col_class)) + + elif nCols == 4: + table_header.append(HT.TH('Index', align='right', width=60, Class=col_class), + HT.TH('Sample', align='right', width=100, Class=col_class), + HT.TH('Value', align='right', width=70, Class=col_class)) + + else: + pass + + if len(attribute_names) > 0: + i=0 + for attribute in attribute_names: + char_count = len(attribute) + cell_width = char_count * 14 + table_header.append(HT.TH(attribute, align='right', width=cell_width, Class="attribute_name " + col_class)) + i+=1 + + return table_header + + + def getSortByValue(self): + + sortby = ("", "") + + return sortby diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py index a63071c3..57c68a1c 100644 --- a/wqflask/wqflask/show_trait/show_trait_page.py +++ b/wqflask/wqflask/show_trait/show_trait_page.py @@ -40,148 +40,148 @@ from DataEditingPage import DataEditingPage class ShowTraitPage(DataEditingPage): - def __init__(self, fd, traitInfos = None): - - #templatePage.__init__(self, fd) - - if not self.openMysql(): - return - - #TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') - print("j2") - # When is traitInfos used? - if traitInfos: - print("j2.2") - database, ProbeSetID, CellID = traitInfos - else: - print("j2.3") - print("fd is:", fd) - database = fd['database'][0] - ProbeSetID = fd['ProbeSetID'][0] - print("j2.4") - CellID = fd.get('CellID') - print("j2.6") - - # We're no longer wrapping this in an exception. If we fail, let's fail hard - # Log it and fix it - #try: - print("j3") - thisTrait = webqtlTrait(db=database, name=ProbeSetID, cellid= CellID, cursor=self.cursor) - #except: - # heading = "Trait Data and Analysis Form" - # detail = ["The trait isn't available currently."] - # self.error(heading=heading,detail=detail,error="Error") - # return - print("j4") - if thisTrait.db.type == "ProbeSet": - - self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers - FROM ProbeSetFreeze WHERE Name = "%s"''' % database) - - indId, indName, indFullName, confidential, AuthorisedUsers = self.cursor.fetchall()[0] - - if confidential == 1: - access_to_confidential_dataset = 0 - - #for the dataset that confidentiality is 1 - #1. 'admin' and 'root' can see all of the dataset - #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table) - if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']: - access_to_confidential_dataset = 1 - else: - AuthorisedUsersList=AuthorisedUsers.split(',') - if AuthorisedUsersList.__contains__(self.userName): - access_to_confidential_dataset = 1 - - if not access_to_confidential_dataset: - #Error, Confidential Database - heading = "Show Database" - detail = ["The %s database you selected is not open to the public \ - at this time, please go back and select other database." % indFullName] - self.error(heading=heading,detail=detail,error="Confidential Database") - return - print("environ:", request.environ) - - # Becuase of proxying remote_addr is probably localhost, so we first try for - # HTTP_X_FORWARDED_FOR - user_ip = request.environ.get('HTTP_X_FORWARDED_FOR') or request.remote_addr # in old app was fd.remote_ip - print("user_ip is:", user_ip) - query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \ - UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400" - self.cursor.execute(query,user_ip) - daycount = self.cursor.fetchall() - if daycount: - daycount = daycount[0][0] - if daycount > webqtlConfig.DAILYMAXIMUM: - heading = "Retrieve Data" - detail = ['For security reasons, the maximum access to a database is \ - %d times per day per ip address. You have reached the limit, please \ - try it again tomorrow.' % webqtlConfig.DAILYMAXIMUM] - self.error(heading=heading,detail=detail) - return - else: - pass - else: - pass - - if thisTrait.db.type != 'ProbeSet' and thisTrait.cellid: - heading = "Retrieve Data" - detail = ['The Record you requested doesn\'t exist!'] - self.error(heading=heading,detail=detail) - return - - #XZ: Aug 23, 2010: I commented out this block because this feature is not used anymore - # check if animal information are available - """ - self.cursor.execute(''' - SELECT - SampleXRef.ProbeFreezeId - FROM - SampleXRef, ProbeSetFreeze - WHERE - SampleXRef.ProbeFreezeId = ProbeSetFreeze.ProbeFreezeId AND - ProbeSetFreeze.Name = "%s" - ''' % thisTrait.db.name) - - sampleId = self.cursor.fetchall() - if sampleId: - thisTrait.strainInfo = 1 - else: - thisTrait.strainInfo = None - """ - - ##identification, etc. - fd.identification = '%s : %s' % (thisTrait.db.shortname,ProbeSetID) - thisTrait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\ - &ProbeSetID=%s&RISet=%s&parentsf1=on' %(database, ProbeSetID, fd['RISet']) - - if CellID: - fd.identification = '%s/%s'%(fd.identification, CellID) - thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL, CellID) - - #retrieve trait information - try: - thisTrait.retrieveInfo() - thisTrait.retrieveData() - self.updMysql() - self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)", user_ip) - self.openMysql() - except Exception as why: - print("Got an exception:", why) - heading = "Retrieve Data" - detail = ["The information you requested is not avaiable at this time."] - self.error(heading=heading, detail=detail) - return - - ##read genotype file - fd.RISet = thisTrait.riset - fd.readGenotype() - - if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())): - fd.displayVariance = 1 - fd.varianceDispName = 'SE' - fd.formID = 'varianceChoice' - - #self.dict['body']= thisTrait - DataEditingPage.__init__(self, fd, thisTrait) - #self.dict['title'] = '%s: Display Trait' % fd.identification + def __init__(self, fd, traitInfos = None): + + #templatePage.__init__(self, fd) + + if not self.openMysql(): + return + + #TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') + print("j2") + # When is traitInfos used? + if traitInfos: + print("j2.2") + database, ProbeSetID, CellID = traitInfos + else: + print("j2.3") + print("fd is:", fd) + database = fd['database'][0] + ProbeSetID = fd['ProbeSetID'][0] + print("j2.4") + CellID = fd.get('CellID') + print("j2.6") + + # We're no longer wrapping this in an exception. If we fail, let's fail hard + # Log it and fix it + #try: + print("j3") + thisTrait = webqtlTrait(db=database, name=ProbeSetID, cellid= CellID, cursor=self.cursor) + #except: + # heading = "Trait Data and Analysis Form" + # detail = ["The trait isn't available currently."] + # self.error(heading=heading,detail=detail,error="Error") + # return + print("j4") + if thisTrait.db.type == "ProbeSet": + + self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers + FROM ProbeSetFreeze WHERE Name = "%s"''' % database) + + indId, indName, indFullName, confidential, AuthorisedUsers = self.cursor.fetchall()[0] + + if confidential == 1: + access_to_confidential_dataset = 0 + + #for the dataset that confidentiality is 1 + #1. 'admin' and 'root' can see all of the dataset + #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table) + if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']: + access_to_confidential_dataset = 1 + else: + AuthorisedUsersList=AuthorisedUsers.split(',') + if AuthorisedUsersList.__contains__(self.userName): + access_to_confidential_dataset = 1 + + if not access_to_confidential_dataset: + #Error, Confidential Database + heading = "Show Database" + detail = ["The %s database you selected is not open to the public \ + at this time, please go back and select other database." % indFullName] + self.error(heading=heading,detail=detail,error="Confidential Database") + return + print("environ:", request.environ) + + # Becuase of proxying remote_addr is probably localhost, so we first try for + # HTTP_X_FORWARDED_FOR + user_ip = request.environ.get('HTTP_X_FORWARDED_FOR') or request.remote_addr # in old app was fd.remote_ip + print("user_ip is:", user_ip) + query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \ + UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400" + self.cursor.execute(query,user_ip) + daycount = self.cursor.fetchall() + if daycount: + daycount = daycount[0][0] + if daycount > webqtlConfig.DAILYMAXIMUM: + heading = "Retrieve Data" + detail = ['For security reasons, the maximum access to a database is \ + %d times per day per ip address. You have reached the limit, please \ + try it again tomorrow.' % webqtlConfig.DAILYMAXIMUM] + self.error(heading=heading,detail=detail) + return + else: + pass + else: + pass + + if thisTrait.db.type != 'ProbeSet' and thisTrait.cellid: + heading = "Retrieve Data" + detail = ['The Record you requested doesn\'t exist!'] + self.error(heading=heading,detail=detail) + return + + #XZ: Aug 23, 2010: I commented out this block because this feature is not used anymore + # check if animal information are available + """ + self.cursor.execute(''' + SELECT + SampleXRef.ProbeFreezeId + FROM + SampleXRef, ProbeSetFreeze + WHERE + SampleXRef.ProbeFreezeId = ProbeSetFreeze.ProbeFreezeId AND + ProbeSetFreeze.Name = "%s" + ''' % thisTrait.db.name) + + sampleId = self.cursor.fetchall() + if sampleId: + thisTrait.strainInfo = 1 + else: + thisTrait.strainInfo = None + """ + + ##identification, etc. + fd.identification = '%s : %s' % (thisTrait.db.shortname,ProbeSetID) + thisTrait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\ + &ProbeSetID=%s&RISet=%s&parentsf1=on' %(database, ProbeSetID, fd['RISet']) + + if CellID: + fd.identification = '%s/%s'%(fd.identification, CellID) + thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL, CellID) + + #retrieve trait information + try: + thisTrait.retrieveInfo() + thisTrait.retrieveData() + self.updMysql() + self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)", user_ip) + self.openMysql() + except Exception as why: + print("Got an exception:", why) + heading = "Retrieve Data" + detail = ["The information you requested is not avaiable at this time."] + self.error(heading=heading, detail=detail) + return + + ##read genotype file + fd.RISet = thisTrait.riset + fd.readGenotype() + + if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())): + fd.displayVariance = 1 + fd.varianceDispName = 'SE' + fd.formID = 'varianceChoice' + + #self.dict['body']= thisTrait + DataEditingPage.__init__(self, fd, thisTrait) + #self.dict['title'] = '%s: Display Trait' % fd.identification -- cgit 1.4.1 From 5ab5ede79ee823f7fbb70016809c887a78732472 Mon Sep 17 00:00:00 2001 From: Sam Ockman Date: Fri, 22 Jun 2012 23:35:30 -0400 Subject: Working my way through getting the review and edit data dynamically generated in Jinja2 --- wqflask/utility/Plot.py | 868 +++++++++++++------------- wqflask/wqflask/show_trait/DataEditingPage.py | 109 ++-- 2 files changed, 497 insertions(+), 480 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 04fe85bf..086f3d57 100755 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -487,440 +487,440 @@ def plotSecurity(canvas, text="12345"): # 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 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' diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index 0194a7d9..38ab8c90 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -7,7 +7,7 @@ from collections import OrderedDict from htmlgen import HTMLgen2 as HT from base import webqtlConfig -from utility import webqtlUtil #, Plot +from utility import webqtlUtil, Plot from base.webqtlTrait import webqtlTrait from dbFunction import webqtlDatabaseFunction from base.templatePage import templatePage @@ -183,7 +183,7 @@ class DataEditingPage(templatePage): ## Trait Value Table ############################# # - #self.dispTraitValues(fd, title5Body, varianceDataPage, nCols, mainForm, thisTrait) + self.dispTraitValues(fd, varianceDataPage, nCols, thisTrait) # if fd.allstrainlist: hddn['allstrainlist'] = string.join(fd.allstrainlist, ' ') @@ -1549,14 +1549,15 @@ class DataEditingPage(templatePage): ########################################## ## Function to display trait tables ########################################## - def dispTraitValues(self, fd , title5Body, varianceDataPage, nCols, mainForm, thisTrait): - traitTableOptions = HT.Div(style="border: 3px solid #EEEEEE; -moz-border-radius: 10px; -webkit-border-radius: 10px; width: 625px; padding: 5px 5px 10px 8px; font-size: 12px; background: #DDDDDD;") - resetButton = HT.Input(type='button',name='resetButton',value=' Reset ',Class="button") - blockSamplesField = HT.Input(type="text",style="background-color:white;border: 1px solid black;font-size: 14px;", name="removeField") - blockSamplesButton = HT.Input(type='button',value=' Block ', name='blockSamples', Class="button") - showHideNoValue = HT.Input(type='button', name='showHideNoValue', value=' Hide No Value ',Class='button') - blockMenuSpan = HT.Span(Id="blockMenuSpan") - blockMenu = HT.Select(name='block_method') + def dispTraitValues(self, fd, varianceDataPage, nCols, thisTrait): + print("in dispTraitValues") + #traitTableOptions = HT.Div(style="border: 3px solid #EEEEEE; -moz-border-radius: 10px; -webkit-border-radius: 10px; width: 625px; padding: 5px 5px 10px 8px; font-size: 12px; background: #DDDDDD;") + #resetButton = HT.Input(type='button',name='resetButton',value=' Reset ',Class="button") + #blockSamplesField = HT.Input(type="text",style="background-color:white;border: 1px solid black;font-size: 14px;", name="removeField") + #blockSamplesButton = HT.Input(type='button',value=' Block ', name='blockSamples', Class="button") + #showHideNoValue = HT.Input(type='button', name='showHideNoValue', value=' Hide No Value ',Class='button') + #blockMenuSpan = HT.Span(Id="blockMenuSpan") + #blockMenu = HT.Select(name='block_method') if fd.genotype.type == "riset": allstrainlist_neworder = fd.f1list + fd.strainlist @@ -1615,21 +1616,21 @@ class DataEditingPage(templatePage): else: pass - showHideOutliers = HT.Input(type='button', name='showHideOutliers', value=' Hide Outliers ', Class='button') - showHideMenuOptions = HT.Span(Id="showHideOptions", style="line-height:225%;") - if other_strains: - pass + #showHideOutliers = HT.Input(type='button', name='showHideOutliers', value=' Hide Outliers ', Class='button') + #showHideMenuOptions = HT.Span(Id="showHideOptions", style="line-height:225%;") + #if other_strains: + # pass #showHideMenuOptions.append(HT.Bold("  Block samples by index:    "), blockSamplesField, "   ", blockMenuSpan, "   ", blockSamplesButton, HT.BR()) - else: - pass + #else: + # pass #showHideMenuOptions.append(HT.Bold("  Block samples by index:    "), blockSamplesField, "   ", blockSamplesButton, HT.BR()) - exportButton = HT.Input(type='button', name='export', value=' Export ', Class='button') + #exportButton = HT.Input(type='button', name='export', value=' Export ', Class='button') if len(attribute_names) > 0: excludeButton = HT.Input(type='button', name='excludeGroup', value=' Block ', Class='button') #showHideMenuOptions.append(HT.Bold("  Block samples by group:"), " "*5, exclude_menu, " "*5) - for menu in dropdown_menus: - pass + #for menu in dropdown_menus: + # pass #showHideMenuOptions.append(menu) #showHideMenuOptions.append(" "*5, excludeButton, HT.BR()) #showHideMenuOptions.append(HT.Bold("  Options:"), " "*5, showHideNoValue, " "*5, showHideOutliers, " "*5, resetButton, " "*5, exportButton) @@ -1652,19 +1653,23 @@ class DataEditingPage(templatePage): other_strainsExist = False for strain in thisTrait.data.keys(): + print("hjl - strain is:", strain) if strain not in allstrainlist_neworder: other_strainsExist = True break + mainForm = None # Just trying to get things working primary_body = self.addTrait2Table(fd=fd, varianceDataPage=varianceDataPage, strainlist=allstrainlist_neworder, mainForm=mainForm, thisTrait=thisTrait, other_strainsExist=other_strainsExist, attribute_ids=attribute_ids, attribute_names=attribute_names, strains='primary') #primary_table.append(primary_header) for i in range(len(primary_body)): + print("hji") pass #primary_table.append(primary_body[i]) other_strains = [] for strain in thisTrait.data.keys(): + print("hjk - strain is:", strain) if strain not in allstrainlist_neworder: pass #allstrainlist_neworder.append(strain) @@ -1697,6 +1702,7 @@ class DataEditingPage(templatePage): #other_table.append(other_header) for i in range(len(other_body)): + print("hjn") pass #other_table.append(other_body[i]) else: @@ -1704,6 +1710,7 @@ class DataEditingPage(templatePage): if other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) \ or (fd.f1list and thisTrait.data.has_key(fd.f1list[1])): + print("hjs") fd.allstrainlist = allstrainlist_neworder ## We put isSE into hddn @@ -1711,7 +1718,7 @@ class DataEditingPage(templatePage): # #mainForm.append(HT.Input(name='isSE', value="yes", type='hidden')) # hddn['isSE'] = "yes" - primary_div = HT.Div(primary_table, Id="primary") #Container for table with primary (for example, BXD) strain values + #primary_div = HT.Div(primary_table, Id="primary") #Container for table with primary (for example, BXD) strain values #container.append(primary_div) if other_strains: @@ -1719,13 +1726,13 @@ class DataEditingPage(templatePage): #container.append(HT.Div(' ', height=30)) #container.append(other_div) - table.append(HT.TR(HT.TD(container))) + #table.append(HT.TR(HT.TD(container))) #title5Body.append(table) def addTrait2Table(self, fd, varianceDataPage, strainlist, mainForm, thisTrait, other_strainsExist=None, attribute_ids=[], attribute_names=[], strains='primary'): #XZ, Aug 23, 2010: I commented the code related to the display of animal case #strainInfo = thisTrait.has_key('strainInfo') and thisTrait.strainInfo - + print("in addTrait2Table") table_body = [] vals = [] @@ -1744,9 +1751,10 @@ class DataEditingPage(templatePage): upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. for i, strainNameOrig in enumerate(strainlist): - + strain = {} + print("zyt - strainNameOrig:", strainNameOrig) trId = strainNameOrig - selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)") + #selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)") strainName = strainNameOrig.replace("_2nd_", "") strainNameAdd = '' @@ -1769,6 +1777,7 @@ class DataEditingPage(templatePage): traitVal = '' dispVal = 'x' + strain['strain_name'] = StrainName strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl') if varianceDataPage: @@ -1806,38 +1815,46 @@ class DataEditingPage(templatePage): # changes it. The updated value is then used when the table is sorted (tablesorter.js). This needs to be done because the "value" attribute is immutable. ######################################################################################################################################################### - valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, - onChange= "javascript:this.form['_2nd_%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) + #valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, + # onChange= "javascript:this.form['_2nd_%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) if varianceDataPage: - seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, - onChange= "javascript:this.form['V_2nd_%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) + pass + #seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, + # onChange= "javascript:this.form['V_2nd_%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) else: - valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, Class=valueClassName) + pass + #valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, Class=valueClassName) if varianceDataPage: - seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, Class=varClassName) + pass + #seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, Class=varClassName) else: - valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVal, - onChange= "javascript:this.form['%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) + pass + #valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVal, + #onChange= "javascript:this.form['%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) if varianceDataPage: - seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, - onChange= "javascript:this.form['V%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) + pass + #seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, + # onChange= "javascript:this.form['V%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) if (strains == 'primary'): - table_row = HT.TR(Id="Primary_"+str(i+1), Class=rowClassName) + strain[the_id] = "Primary_" + str(i+1) + #table_row = HT.TR(Id="Primary_"+str(i+1), Class=rowClassName) else: - table_row = HT.TR(Id="Other_"+str(i+1), Class=rowClassName) + strain[the_id] = "Other_" + str(i+1) + #table_row = HT.TR(Id="Other_"+str(i+1), Class=rowClassName) if varianceDataPage: - table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) - table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) - table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) - table_row.append(HT.TD("±", width=20, align='center', Class=className)) - table_row.append(HT.TD(seField, width=80, align='right', Id="SE_"+str(i)+"_"+strains, Class=className)) + #table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) + #table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) + #table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) + #table_row.append(HT.TD("±", width=20, align='center', Class=className)) + #table_row.append(HT.TD(seField, width=80, align='right', Id="SE_"+str(i)+"_"+strains, Class=className)) + pass else: - table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) - table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) - table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) - + #table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) + #table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) + #table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) + pass if thisTrait and thisTrait.db and thisTrait.db.type =='ProbeSet': if len(attribute_ids) > 0: @@ -1876,7 +1893,7 @@ class DataEditingPage(templatePage): table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) attr_counter += 1 - table_body.append(table_row) + #table_body.append(table_row) return table_body def getTableHeader(self, fd, thisTrait, nCols, attribute_names): -- cgit 1.4.1 From 4cc46d84810ca9492e9a38e1a1f88ab36d214791 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Tue, 28 Aug 2012 16:05:09 -0500 Subject: Various changes related to the webqtlCaseData object and the way values/variances/num_cases are called in DataEditingPage.py --- misc/find.txt | 1 + misc/python_stuff.txt | 1 + wqflask/base/webqtlCaseData.py | 69 ++++-- wqflask/base/webqtlTrait.py | 52 ++-- wqflask/utility/webqtlUtil.py | 7 +- wqflask/wqflask/show_trait/DataEditingPage.py | 276 +++++++++++---------- wqflask/wqflask/show_trait/show_trait_page.py | 27 +- .../wqflask/templates/trait_data_and_analysis.html | 24 +- 8 files changed, 261 insertions(+), 196 deletions(-) create mode 100644 misc/find.txt create mode 100644 misc/python_stuff.txt (limited to 'wqflask/utility') diff --git a/misc/find.txt b/misc/find.txt new file mode 100644 index 00000000..5c792d80 --- /dev/null +++ b/misc/find.txt @@ -0,0 +1 @@ +find | grep _____ diff --git a/misc/python_stuff.txt b/misc/python_stuff.txt new file mode 100644 index 00000000..f36fe338 --- /dev/null +++ b/misc/python_stuff.txt @@ -0,0 +1 @@ +Classes should always inherit "object" \ No newline at end of file diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index f68354be..7805df06 100755 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -24,28 +24,59 @@ # # Last updated by GeneNetwork Core Team 2010/10/20 -class webqtlCaseData: - """ - one case data in one trait - """ +print("Mr. Mojo Risin 2") - val = None #Trait Value - var = None #Trait Variance - N = None #Number of individuals +class webqtlCaseData(object): + """one case data in one trait + + """ - def __init__(self, val=val, var=var, N=N): - self.val = val - self.var = var - self.N = N + def __init__(self, name, value=None, variance=None, num_cases=None): + self.name = name + self.value = value # Trait Value + self.variance = variance # Trait Variance + self.num_cases = num_cases # Number of individuals/cases + self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word) - def __str__(self): + def __repr__(self): str = "" - if self.val != None: - str += "value=%2.3f" % self.val - if self.var != None: - str += " variance=%2.3f" % self.var - if self.N != None: - str += " ndata=%d" % self.N + if self.value != None: + str += "value=%2.3f" % self.value + if self.variance != None: + str += " variance=%2.3f" % self.variance + if self.num_cases != None: + str += " ndata=%d" % self.num_cases return str + + @property + def display_value(self): + if self.value: + return "%2.3f" % self.value + else: + return "x" + + @property + def display_variance(self): + if self.variance: + return "%2.3f" % self.variance + else: + return "x" + + + #try: + # traitVar = thisvar + # dispVar = "%2.3f" % thisvar + #except: + # traitVar = '' + # dispVar = 'x' + + #try: + # traitVal = thisval + # dispVal = "%2.3f" % thisval + #except: + # traitVal = '' + # dispVal = 'x' + - __repr__ = __str__ + #def this_val_full(self): + # strain_name = \ No newline at end of file diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py index 23b98238..337493ef 100755 --- a/wqflask/base/webqtlTrait.py +++ b/wqflask/base/webqtlTrait.py @@ -225,7 +225,10 @@ class webqtlTrait: - def retrieveData(self, strainlist=[]): + def retrieveData(self, strainlist=None): + + if strainlist == None: + strainlist = [] assert self.db and self.cursor if self.db.type == 'Temp': @@ -328,32 +331,33 @@ class webqtlTrait: self.cursor.execute(query) results = self.cursor.fetchall() self.data.clear() + if results: self.mysqlid = results[0][-1] - if strainlist: - for item in results: - if item[0] in strainlist: - val = item[1] - if val != None: - var = item[2] - ndata = None - if self.db.type in ('Publish', 'Temp'): - ndata = item[3] - self.data[item[0]] = webqtlCaseData(val, var, ndata) + #if strainlist: + for item in results: + #name, value, variance, num_cases = item + if not strainlist or (strainlist and name in strainlist): + #if value != None: + # num_cases = None + # if self.db.type in ('Publish', 'Temp'): + # ndata = item[3] + name = item[0] + self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) #end for - else: - for item in results: - val = item[1] - if val != None: - var = item[2] - ndata = None - if self.db.type in ('Publish', 'Temp'): - ndata = item[3] - self.data[item[0]] = webqtlCaseData(val, var, ndata) - #end for - #end if - else: - pass + # else: + # for item in results: + # val = item[1] + # if val != None: + # var = item[2] + # ndata = None + # if self.db.type in ('Publish', 'Temp'): + # ndata = item[3] + # self.data[item[0]] = webqtlCaseData(val, var, ndata) + # #end for + # #end if + #else: + # pass def keys(self): return self.__dict__.keys() diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index 6409e781..99451e33 100755 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -252,7 +252,12 @@ def FloatList2String(lst): return "" def ListNotNull(lst): - 'Determine if the elements in a list are all null' + '''Obsolete - Use built in function any (or all or whatever) + + + Determine if the elements in a list are all null + + ''' for item in lst: if item is not None: return 1 diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index f9133f27..43f05f14 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -11,6 +11,7 @@ import yaml from htmlgen import HTMLgen2 as HT from base import webqtlConfig +from base import webqtlCaseData from utility import webqtlUtil, Plot from base.webqtlTrait import webqtlTrait from dbFunction import webqtlDatabaseFunction @@ -172,17 +173,17 @@ class DataEditingPage(templatePage): if thisTrait == None: thisTrait = webqtlTrait(data=fd.allTraitData, db=None) - # Variance submit page only - if fd.enablevariance and not varianceDataPage: - pass - #title2Body.append("Click the next button to go to the variance submission form.", - # HT.Center(next,reset)) - else: - pass - # We'll get this part working later - print("Calling dispBasicStatistics") - self.dispBasicStatistics(fd, thisTrait) - #self.dispMappingTools(fd, title4Body, thisTrait) + ## Variance submit page only + #if fd.enablevariance and not varianceDataPage: + # pass + # #title2Body.append("Click the next button to go to the variance submission form.", + # # HT.Center(next,reset)) + #else: + # pass + # # We'll get this part working later + # print("Calling dispBasicStatistics") + # self.dispBasicStatistics(fd, thisTrait) + # #self.dispMappingTools(fd, title4Body, thisTrait) ############################# ## Trait Value Table @@ -892,13 +893,13 @@ class DataEditingPage(templatePage): for strain in thisTrait.data.keys(): strainName = strain.replace("_2nd_", "") if strain not in strainlist: - if (thisTrait.data[strainName].val != None): + if thisTrait.data[strainName].value != None: if strain.find('F1') < 0: specialStrains.append(strain) - if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)): + if (thisTrait.data[strainName].value != None) and (strain not in (fd.f1list + fd.parlist)): other_strains.append(strain) #XZ: at current stage, other_strains doesn't include parent strains and F1 strains of primary group else: - if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)): + if (thisTrait.data[strainName].value != None) and (strain not in (fd.f1list + fd.parlist)): primary_strains.append(strain) #XZ: at current stage, the primary_strains is the same as fd.strainlist / ZS: I tried defining primary_strains as fd.strainlist instead, but in some cases it ended up including the parent strains (1436869_at BXD) if len(other_strains) > 3: @@ -941,41 +942,58 @@ class DataEditingPage(templatePage): vals3 = [] #Using all strains/cases for values - for i, strainNameOrig in enumerate(all_strains): + #for strain_type in (all_strains, primary_strains, other_strains): + for strainNameOrig in all_strains: strainName = strainNameOrig.replace("_2nd_", "") - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName, thisval, thisvar] - except: - continue + #try: + print("* type of thisTrait:", type(thisTrait)) + print(" name:", thisTrait.__class__.__name__) + print(" thisTrait:", thisTrait) + print(" type of thisTrait.data[strainName]:", type(thisTrait.data[strainName])) + print(" name:", thisTrait.data[strainName].__class__.__name__) + print(" thisTrait.data[strainName]:", thisTrait.data[strainName]) + thisval = thisTrait.data[strainName].value + print(" thisval:", thisval) + thisvar = thisTrait.data[strainName].variance + print(" thisvar:", thisvar) + thisValFull = [strainName, thisval, thisvar] + print(" thisValFull:", thisValFull) + #except: + # continue vals1.append(thisValFull) + + + #vals1 = [[strainNameOrig.replace("_2nd_", ""), + # thisTrait.data[strainName].val, + # thisTrait.data[strainName].var] + # for strainNameOrig in all_strains]] + # #Using just the RISet strain - for i, strainNameOrig in enumerate(primary_strains): + for strainNameOrig in primary_strains: strainName = strainNameOrig.replace("_2nd_", "") - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue + #try: + thisval = thisTrait.data[strainName].value + thisvar = thisTrait.data[strainName].variance + thisValFull = [strainName,thisval,thisvar] + #except: + # continue vals2.append(thisValFull) #Using all non-RISet strains only - for i, strainNameOrig in enumerate(other_strains): + for strainNameOrig in other_strains: strainName = strainNameOrig.replace("_2nd_", "") - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue + #try: + thisval = thisTrait.data[strainName].value + thisvar = thisTrait.data[strainName].variance + thisValFull = [strainName,thisval,thisvar] + #except: + # continue vals3.append(thisValFull) @@ -985,15 +1003,15 @@ class DataEditingPage(templatePage): vals = [] #Using all strains/cases for values - for i, strainNameOrig in enumerate(all_strains): + for strainNameOrig in all_strains: strainName = strainNameOrig.replace("_2nd_", "") - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue + #try: + thisval = thisTrait.data[strainName].value + thisvar = thisTrait.data[strainName].variance + thisValFull = [strainName,thisval,thisvar] + #except: + # continue vals.append(thisValFull) @@ -1344,24 +1362,26 @@ class DataEditingPage(templatePage): # updated by NL 5-28-2010 # Interval Mapping chrMenu = HT.Select(name='chromosomes1') - chrMenu.append(tuple(["All",-1])) + chrMenu.append(("All",-1)) for i in range(len(fd.genotype)): - if len(fd.genotype[i]) > 1: - chrMenu.append(tuple([fd.genotype[i].name,i])) + if len(fd.genotype[i]) > 1: + chrMenu.append((fd.genotype[i].name, i)) #Menu for Composite Interval Mapping chrMenu2 = HT.Select(name='chromosomes2') - chrMenu2.append(tuple(["All",-1])) + chrMenu2.append(("All",-1)) for i in range(len(fd.genotype)): - if len(fd.genotype[i]) > 1: - chrMenu2.append(tuple([fd.genotype[i].name,i])) + if len(fd.genotype[i]) > 1: + chrMenu2.append((fd.genotype[i].name, i)) if fd.genotype.Mbmap: scaleText = HT.Span("Mapping Scale:", Class="ffl fwb fs12") - scaleMenu1 = HT.Select(name='scale1', onChange="checkUncheck(window.document.dataInput.scale1.value, window.document.dataInput.permCheck1, window.document.dataInput.bootCheck1)") + scaleMenu1 = HT.Select(name='scale1', + onChange="checkUncheck(window.document.dataInput.scale1.value, window.document.dataInput.permCheck1, window.document.dataInput.bootCheck1)") scaleMenu1.append(("Megabase",'physic')) scaleMenu1.append(("Centimorgan",'morgan')) - scaleMenu2 = HT.Select(name='scale2', onChange="checkUncheck(window.document.dataInput.scale2.value, window.document.dataInput.permCheck2, window.document.dataInput.bootCheck2)") + scaleMenu2 = HT.Select(name='scale2', + onChange="checkUncheck(window.document.dataInput.scale2.value, window.document.dataInput.permCheck2, window.document.dataInput.bootCheck2)") scaleMenu2.append(("Megabase",'physic')) scaleMenu2.append(("Centimorgan",'morgan')) @@ -1521,7 +1541,7 @@ class DataEditingPage(templatePage): submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") - if mappingMethodId != None: + if not mappingMethodId: if int(mappingMethodId) == 1: submitTable.append(mapping_row) submitTable.append(mapping_script) @@ -1567,17 +1587,6 @@ class DataEditingPage(templatePage): title4Body.append(submitTable) - def natural_sort(strain_list): - - sorted = [] - for strain in strain_list: - try: - strain = int(strain) - try: sorted[-1] = sorted[-1] * 10 + strain - except: sorted.append(strain) - except: - sorted.append(strain) - return sorted ########################################## ## Function to display trait tables @@ -1727,8 +1736,9 @@ class DataEditingPage(templatePage): attribute_names=attribute_names, strains='other') - if other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) \ - or (fd.f1list and thisTrait.data.has_key(fd.f1list[1])): + #TODO: Figure out why this if statement is written this way - Zach + if (other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) + or (fd.f1list and thisTrait.data.has_key(fd.f1list[1]))): print("hjs") fd.allstrainlist = allstrainlist_neworder @@ -1738,85 +1748,93 @@ class DataEditingPage(templatePage): def addTrait2Table(self, fd, varianceDataPage, strainlist, mainForm, thisTrait, - other_strainsExist=None, attribute_ids=[], - attribute_names=[], strains='primary'): + other_strainsExist=None, attribute_ids=None, + attribute_names=None, strains='primary'): + + if attribute_ids == None: + attribute_ids = [] + + if attribute_names == None: + attribute_names = [] + #XZ, Aug 23, 2010: I commented the code related to the display of animal case #strainInfo = thisTrait.has_key('strainInfo') and thisTrait.strainInfo print("in addTrait2Table") table_body = [] vals = [] - for i, strainNameOrig in enumerate(strainlist): - strainName = strainNameOrig.replace("_2nd_", "") - - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue - - vals.append(thisValFull) - upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. + #################### Only used to find upperBound and lowerBound + #for strainNameOrig in strainlist: + # strainName = strainNameOrig.replace("_2nd_", "") + # print("pen: %s - %s" % (strainNameOrig, strainName)) + # thisval = thisTrait.data[strainName].value + # thisvar = thisTrait.data[strainName].variance + # thisValFull = [strainName, thisval, thisvar] + # + # vals.append(thisValFull) + # + #upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. the_strains = [] - for i, strainNameOrig in enumerate(strainlist): - strain = {} - print("zyt - strainNameOrig:", strainNameOrig) - trId = strainNameOrig - #selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)") - + for counter, strainNameOrig in enumerate(strainlist, 1): strainName = strainNameOrig.replace("_2nd_", "") strainNameAdd = '' if fd.RISet == 'AXBXA' and strainName in ('AXB18/19/20','AXB13/14','BXA8/17'): strainNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") - + try: - thisval, thisvar, thisNP = thisTrait.data[strainName].val, thisTrait.data[strainName].var, thisTrait.data[strainName].N - if thisNP: - mainForm.append(HT.Input(name='N'+strainName, value=thisNP, type='hidden')) - else: - pass - except: - thisval = thisvar = 'x' - - try: - traitVal = thisval - dispVal = "%2.3f" % thisval - except: - traitVal = '' - dispVal = 'x' + strain = thisTrait.data[strainName] + except KeyError: + print("No strain %s, let's create it now" % strainName) + strain = webqtlCaseData.webqtlCaseData(strainName) + print("zyt - strainNameOrig:", strainNameOrig) + #trId = strainNameOrig + #selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)") - strain['strain_name'] = strainName - strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl') + + #try: + # thisval, thisvar, thisNP = thisTrait.data[strainName].value, thisTrait.data[strainName].var, thisTrait.data[strainName].N + # if thisNP: + # mainForm.append(HT.Input(name='N'+strainName, value=thisNP, type='hidden')) + # else: + # pass + #except: + # thisval = thisvar = 'x' - if varianceDataPage: - try: - traitVar = thisvar - dispVar = "%2.3f" % thisvar - except: - traitVar = '' - dispVar = 'x' + #thisval = thisTrait.data[strainName].value + #thisvar = thisTrait.data[strainName].variance + #thisTrait.data[strainName].num_cases - if thisval == 'x': - traitVar = '' #ZS: Used to be 0, but it doesn't seem like a good idea for values of 0 to *always* be at the bottom when you sort; it makes more sense to put "nothing" + #strain['strain_name'] = strainName + #strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl') - #className = 'fs13 b1 c222 ' - #valueClassName = 'fs13 b1 c222 valueField ' - #rowClassName = 'novalue ' - else: - if (thisval >= upperBound) or (thisval <= lowerBound): - strain['outlier'] = "outlier" # We're going to use this as a class, so we want it to be a word - #className = 'fs13 b1 c222 outlier ' - #valueClassName = 'fs13 b1 c222 valueField ' - #rowClassName = 'outlier' - else: - strain['outlier'] = "not_outlier" - #className = 'fs13 b1 c222 ' - #valueClassName = 'fs13 b1 c222 valueField ' - #rowClassName = ' ' + #if varianceDataPage: + #try: + # traitVar = thisvar + # dispVar = "%2.3f" % thisvar + #except: + # traitVar = '' + # dispVar = 'x' + + #if thisval == 'x': + # traitVar = '' #ZS: Used to be 0, but it doesn't seem like a good idea for values of 0 to *always* be at the bottom when you sort; it makes more sense to put "nothing" + # + # #className = 'fs13 b1 c222 ' + # #valueClassName = 'fs13 b1 c222 valueField ' + # #rowClassName = 'novalue ' + #else: + # if (thisval >= upperBound) or (thisval <= lowerBound): + # strain['outlier'] = "outlier" # We're going to use this as a class, so we want it to be a word + # #className = 'fs13 b1 c222 outlier ' + # #valueClassName = 'fs13 b1 c222 valueField ' + # #rowClassName = 'outlier' + # else: + # strain['outlier'] = "not_outlier" + # #className = 'fs13 b1 c222 ' + # #valueClassName = 'fs13 b1 c222 valueField ' + # #rowClassName = ' ' # #if varianceDataPage: # varClassName = valueClassName + str(traitVar) @@ -1851,15 +1869,15 @@ class DataEditingPage(templatePage): # # onChange= "javascript:this.form['V%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) if strains == 'primary': - strain['the_id'] = "Primary_" + str(i+1) + strain.this_id = "Primary_" + str(counter) #table_row = HT.TR(Id="Primary_"+str(i+1), Class=rowClassName) else: - strain['the_id'] = "Other_" + str(i+1) + strain.this_id = "Other_" + str(counter) #table_row = HT.TR(Id="Other_"+str(i+1), Class=rowClassName) - strain['value'] = traitVal - - strain['se'] = dispVar + #strain['value'] = traitVal + # + #strain['se'] = dispVar #if varianceDataPage: #table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) #table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py index b1f71e55..b42f5e8e 100644 --- a/wqflask/wqflask/show_trait/show_trait_page.py +++ b/wqflask/wqflask/show_trait/show_trait_page.py @@ -161,24 +161,25 @@ class ShowTraitPage(DataEditingPage): thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL, CellID) #retrieve trait information - try: - thisTrait.retrieveInfo() - thisTrait.retrieveData() - self.updMysql() - self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)", user_ip) - self.openMysql() - except Exception as why: - print("Got an exception:", why) - heading = "Retrieve Data" - detail = ["The information you requested is not avaiable at this time."] - self.error(heading=heading, detail=detail) - return + #try: + thisTrait.retrieveInfo() + thisTrait.retrieveData() + self.updMysql() + self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)", user_ip) + self.openMysql() + #except Exception as why: + # print("Got an exception:", why) + # heading = "Retrieve Data" + # detail = ["The information you requested is not avaiable at this time."] + # self.error(heading=heading, detail=detail) + # return ##read genotype file fd.RISet = thisTrait.riset fd.readGenotype() - if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())): + #if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())): + if any([x.variance for x in thisTrait.data.values()]): fd.displayVariance = 1 fd.varianceDispName = 'SE' fd.formID = 'varianceChoice' diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html index 4bf06d45..94ba0aad 100644 --- a/wqflask/wqflask/templates/trait_data_and_analysis.html +++ b/wqflask/wqflask/templates/trait_data_and_analysis.html @@ -8,7 +8,7 @@
-
+
{# @@ -3059,7 +3059,7 @@
{% for strain_type in (primary_strains, other_strains) %} -
{# Slightly tortuous, but best way to get the id we need #} +
{# Slightly tortuous, but best way to get the id we need #} @@ -3076,20 +3076,20 @@ {% for strain in strain_type %} - + {# Todo: Add IDs #} @@ -3099,8 +3099,8 @@ {# Todo: Add IDs #} {% endfor %} @@ -3133,4 +3133,8 @@ - {% endblock %} + + + + + {% endblock %} -- cgit 1.4.1 From be095620bc8126026514fdee43e06a9a9f443f97 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Wed, 29 Aug 2012 17:49:43 -0500 Subject: Fixed so that outliers are now correctly highlighted --- wqflask/base/webqtlCaseData.py | 26 ++-- wqflask/utility/Plot.py | 100 ++++++------- wqflask/wqflask/show_trait/DataEditingPage.py | 154 ++++++--------------- .../wqflask/templates/trait_data_and_analysis.html | 2 +- 4 files changed, 103 insertions(+), 179 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 7805df06..25665c55 100755 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -37,6 +37,7 @@ class webqtlCaseData(object): self.variance = variance # Trait Variance self.num_cases = num_cases # Number of individuals/cases self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word) + self.outlier = None # Not set to True/False until later def __repr__(self): str = "" @@ -48,6 +49,14 @@ class webqtlCaseData(object): str += " ndata=%d" % self.num_cases return str + @property + def class_outlier(self): + """Template helper""" + if self.outlier: + return "outlier" + else: + return "" + @property def display_value(self): if self.value: @@ -63,20 +72,3 @@ class webqtlCaseData(object): return "x" - #try: - # traitVar = thisvar - # dispVar = "%2.3f" % thisvar - #except: - # traitVar = '' - # dispVar = 'x' - - #try: - # traitVal = thisval - # dispVal = "%2.3f" % thisval - #except: - # traitVal = '' - # dispVal = 'x' - - - #def this_val_full(self): - # strain_name = \ No newline at end of file diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 086f3d57..51a57a6d 100755 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -25,6 +25,13 @@ # Last updated by GeneNetwork Core Team 2010/10/20 #import piddle as pid + +from __future__ import print_function + +from pprint import pformat as pf + +print("Lysol") + from math import * import random import sys, os @@ -32,6 +39,9 @@ from numarray import linear_algebra as la from numarray import ones, array, dot, swapaxes import reaper +sys.path.append("..") +print(sys.path) +from basicStatistics import corestats import svg import webqtlUtil @@ -254,6 +264,7 @@ def gmedian(lst2): return lst[(N-1)/2] def gpercentile(lst2, np): + """Obsolete - use percentile in corestats instead""" lst = lst2[:] N = len(lst) if N == 0 or np > 100 or np < 0: @@ -270,61 +281,41 @@ def gpercentile(lst2, np): 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) +def find_outliers(vals): + """Calculates the upper and lower bounds of a set of sample/case values + + + >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537]) + (11.252500000000001, 0.5364999999999993) + + >>> >>> find_outliers([9,12,15,17,31,50,7,5,6,8]) + (32.0, -8.0) + + If there are no vals, returns None for the upper and lower bounds, + which code that calls it will have to deal with. + >>> find_outliers([]) + (None, None) + + """ - outlier = [] - extreme = [] + print("xerxes vals is:", pf(vals)) - upperBound = upHinge + Hstep - lowerBound = lowHinge - Hstep + if vals: + #print("vals is:", pf(vals)) + stats = corestats.Stats(vals) + low_hinge = stats.percentile(25) + up_hinge = stats.percentile(75) + hstep = 1.5 * (up_hinge - low_hinge) - for item in catValue: - if item >= upHinge + 2*Hstep: - extreme.append(item) - elif item >= upHinge + Hstep: - outlier.append(item) - else: - pass + upper_bound = up_hinge + hstep + lower_bound = low_hinge - hstep - 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 + else: + upper_bound = None + lower_bound = None - return upperBound, lowerBound + print(pf(locals())) + return upper_bound, lower_bound def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabel="Value"): @@ -1281,3 +1272,12 @@ def BWSpectrum(n=100): out.append(pid.Color(x,x,x)); x += step return out + + +def _test(): + import doctest + doctest.testmod() + + +if __name__=="__main__": + _test() diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index 43f05f14..bb6156c3 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -1,5 +1,7 @@ from __future__ import absolute_import, print_function, division +print("Google") + import string import os import cPickle @@ -1673,7 +1675,7 @@ class DataEditingPage(templatePage): #showHideMenuOptions.append(HT.Bold("  Options:"), " "*5, showHideNoValue, " "*5, showHideOutliers, " "*5, resetButton, " "*5, exportButton) #traitTableOptions.append(showHideMenuOptions,HT.BR(),HT.BR()) - #traitTableOptions.append(HT.Span("  Outliers highlighted in ", HT.Bold(" yellow ", style="background-color:yellow;"), " can be hidden using the ", + #traitTableOptions.append(HT.Span("  Outliers highlighted in ", HT.Bold(" red ", style="background-color:red;"), " can be hidden using the ", # HT.Strong(" Hide Outliers "), " button,",HT.BR(),"  and samples with no value (x) can be hidden by clicking ", # HT.Strong(" Hide No Value "), "."), HT.BR()) @@ -1703,7 +1705,7 @@ class DataEditingPage(templatePage): primary_strainlist = fd.parlist + allstrainlist_neworder - primary_strains = self.addTrait2Table(fd=fd, + primary_strains = self.create_strain_objects(fd=fd, varianceDataPage=varianceDataPage, strainlist=primary_strainlist, mainForm=mainForm, @@ -1712,6 +1714,7 @@ class DataEditingPage(templatePage): attribute_ids=attribute_ids, attribute_names=attribute_names, strains='primary') + other_strains = [] for strain in thisTrait.data.keys(): @@ -1727,7 +1730,7 @@ class DataEditingPage(templatePage): other_strains.sort() #Sort other strains other_strains = par_f1_strains + other_strains - other_strains = self.addTrait2Table(fd=fd, + other_strains = self.create_strain_objects(fd=fd, varianceDataPage=varianceDataPage, strainlist=other_strains, mainForm=mainForm, @@ -1736,6 +1739,7 @@ class DataEditingPage(templatePage): attribute_names=attribute_names, strains='other') + #TODO: Figure out why this if statement is written this way - Zach if (other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) or (fd.f1list and thisTrait.data.has_key(fd.f1list[1]))): @@ -1747,7 +1751,7 @@ class DataEditingPage(templatePage): self.other_strains = other_strains - def addTrait2Table(self, fd, varianceDataPage, strainlist, mainForm, thisTrait, + def create_strain_objects(self, fd, varianceDataPage, strainlist, mainForm, thisTrait, other_strainsExist=None, attribute_ids=None, attribute_names=None, strains='primary'): @@ -1759,23 +1763,26 @@ class DataEditingPage(templatePage): #XZ, Aug 23, 2010: I commented the code related to the display of animal case #strainInfo = thisTrait.has_key('strainInfo') and thisTrait.strainInfo - print("in addTrait2Table") - table_body = [] - vals = [] - - - #################### Only used to find upperBound and lowerBound + print("in create_strain_objects") + #table_body = [] + + ################### Only used to find upperBound and lowerBound + #vals = [] #for strainNameOrig in strainlist: # strainName = strainNameOrig.replace("_2nd_", "") # print("pen: %s - %s" % (strainNameOrig, strainName)) - # thisval = thisTrait.data[strainName].value - # thisvar = thisTrait.data[strainName].variance - # thisValFull = [strainName, thisval, thisvar] - # - # vals.append(thisValFull) + # try: + # thisval = thisTrait.data[strainName].value + # thisvar = thisTrait.data[strainName].variance + # thisValFull = [strainName, thisval, thisvar] + # + # vals.append(thisValFull) + # except KeyError: + # print("**x** Skipping:", strainName) # #upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. + the_strains = [] for counter, strainNameOrig in enumerate(strainlist, 1): @@ -1790,107 +1797,15 @@ class DataEditingPage(templatePage): print("No strain %s, let's create it now" % strainName) strain = webqtlCaseData.webqtlCaseData(strainName) print("zyt - strainNameOrig:", strainNameOrig) - #trId = strainNameOrig - #selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)") - - - #try: - # thisval, thisvar, thisNP = thisTrait.data[strainName].value, thisTrait.data[strainName].var, thisTrait.data[strainName].N - # if thisNP: - # mainForm.append(HT.Input(name='N'+strainName, value=thisNP, type='hidden')) - # else: - # pass - #except: - # thisval = thisvar = 'x' - - #thisval = thisTrait.data[strainName].value - #thisvar = thisTrait.data[strainName].variance - #thisTrait.data[strainName].num_cases - - #strain['strain_name'] = strainName - #strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl') - - #if varianceDataPage: - #try: - # traitVar = thisvar - # dispVar = "%2.3f" % thisvar - #except: - # traitVar = '' - # dispVar = 'x' - - #if thisval == 'x': - # traitVar = '' #ZS: Used to be 0, but it doesn't seem like a good idea for values of 0 to *always* be at the bottom when you sort; it makes more sense to put "nothing" - # - # #className = 'fs13 b1 c222 ' - # #valueClassName = 'fs13 b1 c222 valueField ' - # #rowClassName = 'novalue ' - #else: - # if (thisval >= upperBound) or (thisval <= lowerBound): - # strain['outlier'] = "outlier" # We're going to use this as a class, so we want it to be a word - # #className = 'fs13 b1 c222 outlier ' - # #valueClassName = 'fs13 b1 c222 valueField ' - # #rowClassName = 'outlier' - # else: - # strain['outlier'] = "not_outlier" - # #className = 'fs13 b1 c222 ' - # #valueClassName = 'fs13 b1 c222 valueField ' - # #rowClassName = ' ' - # - #if varianceDataPage: - # varClassName = valueClassName + str(traitVar) - #valueClassName += str(traitVal) - - #if strainNameOrig == strainName: - # if other_strainsExist and strainNameOrig in (fd.parlist + fd.f1list): - # ######################################################################################################################################################## - # # ZS: Append value and variance to the value and variance input fields' list of classes; this is so the javascript can update the value when the user - # # changes it. The updated value is then used when the table is sorted (tablesorter.js). This needs to be done because the "value" attribute is immutable. - # ######################################################################################################################################################### - # - # #valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, - # # onChange= "javascript:this.form['_2nd_%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) - # if varianceDataPage: - # pass - # #seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, - # # onChange= "javascript:this.form['V_2nd_%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) - # else: - # pass - # #valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, Class=valueClassName) - # if varianceDataPage: - # pass - # #seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, Class=varClassName) - #else: - # pass - # #valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVal, - # #onChange= "javascript:this.form['%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) - # if varianceDataPage: - # pass - # #seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, - # # onChange= "javascript:this.form['V%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) + if strains == 'primary': strain.this_id = "Primary_" + str(counter) - #table_row = HT.TR(Id="Primary_"+str(i+1), Class=rowClassName) else: strain.this_id = "Other_" + str(counter) - #table_row = HT.TR(Id="Other_"+str(i+1), Class=rowClassName) - - #strain['value'] = traitVal - # - #strain['se'] = dispVar - #if varianceDataPage: - #table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) - #table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) - #table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) - #table_row.append(HT.TD("±", width=20, align='center', Class=className)) - #table_row.append(HT.TD(seField, width=80, align='right', Id="SE_"+str(i)+"_"+strains, Class=className)) - #pass - #else: - #table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) - #table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) - #table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) - #pass - if thisTrait and thisTrait.db and thisTrait.db.type =='ProbeSet': + + #### For extra attribute columns; currently only used by two human datasets - Zach + if thisTrait and thisTrait.db and thisTrait.db.type == 'ProbeSet': if len(attribute_ids) > 0: #ZS: Get StrainId value for the next query @@ -1929,6 +1844,8 @@ class DataEditingPage(templatePage): attr_counter += 1 the_strains.append(strain) #table_body.append(table_row) + + do_outliers(the_strains) print("*the_strains are [%i]: %s" % (len(the_strains), pf(the_strains))) return the_strains @@ -1975,3 +1892,18 @@ class DataEditingPage(templatePage): sortby = ("", "") return sortby + + + +def do_outliers(strain_objects): + values = [strain.value for strain in strain_objects if strain.value != None] + upper_bound, lower_bound = Plot.find_outliers(values) + + for strain in strain_objects: + if strain.value: + if upper_bound and strain.value > upper_bound: + strain.outlier = True + elif lower_bound and strain.value < lower_bound: + strain.outlier = True + else: + strain.outlier = False diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html index 94ba0aad..3644b436 100644 --- a/wqflask/wqflask/templates/trait_data_and_analysis.html +++ b/wqflask/wqflask/templates/trait_data_and_analysis.html @@ -3076,7 +3076,7 @@ {% for strain in strain_type %} - +
{{ loop.index }} - + - {{ strain.strain_name }} + {{ strain.name }} - -
{{ loop.index }} -- cgit 1.4.1 From 720a13ae3ab8fda14f41a02374480574e27df890 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Wed, 26 Sep 2012 17:42:43 -0500 Subject: Worked on implementing the extra attributes feature on the trait data page --- wqflask/utility/__init__.py | 12 ++ wqflask/wqflask/show_trait/DataEditingPage.py | 264 ++++++++++++++------------ 2 files changed, 156 insertions(+), 120 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index e69de29b..206d0d1c 100755 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -0,0 +1,12 @@ +class Bunch(object): + """Make the configuration a little cleaner""" + def __init__(self, config_string = "", **kw): + if config_string: + td = yaml.load(config_string) + self.__dict__.update(td) + else: + self.__dict__ = kw + + def __repr__(self): + return yaml.dump(self.__dict__, default_flow_style=False) + diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index d186889b..e431fd76 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -12,7 +12,7 @@ from htmlgen import HTMLgen2 as HT from base import webqtlConfig from base import webqtlCaseData -from utility import webqtlUtil, Plot +from utility import webqtlUtil, Plot, Bunch from base.webqtlTrait import webqtlTrait from dbFunction import webqtlDatabaseFunction from base.templatePage import templatePage @@ -1467,9 +1467,6 @@ class DataEditingPage(templatePage): all_samples_ordered = fd.f1list + fd.samplelist else: all_samples_ordered = fd.f1list + fd.parlist + fd.samplelist - - attribute_ids = [] - attribute_names = [] #ZS: Id values for this trait's extra attributes; #used to create "Exclude" dropdown and query for attribute values and create @@ -1479,6 +1476,8 @@ class DataEditingPage(templatePage): CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId group by CaseAttributeXRef.CaseAttributeId""", (str(this_trait.db.id),)) + + for this_attr_name in attribute_names: # Todo: Needs testing still! @@ -1491,36 +1490,28 @@ class DataEditingPage(templatePage): distinct_values = self.cursor.fetchall() this_trait_samples = set(this_trait.data.keys()) - #ZS - Checks if there are any samples in this_trait_samples that aren't in all_samples_ordered - #Will need to be used in the future to determine whether to create one or two tables are created (probably) - #other_samples_exist = this_trait_samples - set(all_samples_ordered) - #mainForm = None # Just trying to get things working + primary_sample_names = all_samples_ordered - primary_samplelist = all_samples_ordered - - print("primary_samplelist is:", pf(primary_samplelist)) + print("primary_samplelist is:", pf(primary_sample_names)) primary_samples = SampleList(self.cursor, - fd=fd, - variance_data_page=variance_data_page, - samplelist=primary_samplelist, - #mainForm=mainForm, - this_trait=this_trait, - attribute_ids=attribute_ids, - attribute_names=attribute_names, - samples='primary', - header="%s Only" % (fd.RISet)) - - - other_samples = [] + fd=fd, + variance_data_page=variance_data_page, + sample_names=primary_sample_names, + this_trait=this_trait, + samples='primary', + header="%s Only" % (fd.RISet)) + + + other_sample_names = [] for sample in this_trait.data.keys(): print("hjk - sample is:", sample) if sample not in all_samples_ordered: all_samples_ordered.append(sample) - other_samples.append(sample) + other_sample_names.append(sample) - if other_samples: + if other_sample_names: unappended_par_f1 = fd.f1list + fd.parlist par_f1_samples = ["_2nd_" + sample for sample in unappended_par_f1] @@ -1528,31 +1519,24 @@ class DataEditingPage(templatePage): other_samples = par_f1_samples + other_samples other_samples = SampleList(self.cursor, - fd=fd, - variance_data_page=variance_data_page, - samplelist=other_samples, - #mainForm=mainForm, - this_trait=this_trait, - attribute_ids=attribute_ids, - attribute_names=attribute_names, - samples='other', - header="Non-%s" % (fd.RISet)) - + fd=fd, + variance_data_page=variance_data_page, + sample_names=other_sample_names, + this_trait=this_trait, + samples='other', + header="Non-%s" % (fd.RISet)) + + self.sample_groups = (primary_samples, other_samples) + else: + self.sample_groups = (primary_samples,) #TODO: Figure out why this if statement is written this way - Zach - if (other_samples or (fd.f1list and this_trait.data.has_key(fd.f1list[0])) + if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0])) or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))): print("hjs") fd.allsamplelist = all_samples_ordered - - - #self.primary_samples = dict(header = "%s Only" % (fd.RISet), - # samples = primary_samples,) - # - #self.other_samples = dict(header = "Non-%s" % (fd.RISet), - # samples = other_samples,) - self.sample_groups = (primary_samples, other_samples) + class SampleList(list): @@ -1560,56 +1544,35 @@ class SampleList(list): cursor, fd, variance_data_page, - samplelist, + sample_names, this_trait, - attribute_ids, - attribute_names, samples, header): self.header = header - - if attribute_ids == None: - attribute_ids = [] - - if attribute_names == None: - attribute_names = [] - - #XZ, Aug 23, 2010: I commented the code related to the display of animal case - #sampleInfo = this_trait.has_key('sampleInfo') and this_trait.sampleInfo - print("in create_sample_objects") - #table_body = [] - ################### Only used to find upperBound and lowerBound - #vals = [] - #for sampleNameOrig in samplelist: - # sampleName = sampleNameOrig.replace("_2nd_", "") - # print("pen: %s - %s" % (sampleNameOrig, sampleName)) - # try: - # thisval = this_trait.data[sampleName].value - # thisvar = this_trait.data[sampleName].variance - # thisValFull = [sampleName, thisval, thisvar] - # - # vals.append(thisValFull) - # except KeyError: - # print("**x** Skipping:", sampleName) - # - #upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. - + + + self.calc_attributes() - #the_samples = [] + for counter, sample_name in enumerate(sample_names, 1): + sample_name = sample_name.replace("_2nd_", "") - for counter, sampleNameOrig in enumerate(samplelist, 1): - sampleName = sampleNameOrig.replace("_2nd_", "") - sampleNameAdd = '' - if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'): - sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") - + #ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table) try: - sample = this_trait.data[sampleName] + sample = this_trait.data[sample_name] except KeyError: - print("No sample %s, let's create it now" % sampleName) - sample = webqtlCaseData.webqtlCaseData(sampleName) + print("No sample %s, let's create it now" % sample_name) + sample = webqtlCaseData.webqtlCaseData(sample_name) + + #sampleNameAdd = '' + #if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'): + # sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") + sample.extra_info = {} + if fd.RISet == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'): + sample.extra_info['url'] = "/mouseCross.html#AXB/BXA" + sample.extra_info['css_class'] = "fs12" + print("zyt - sampleNameOrig:", sampleNameOrig) print(" type of sample:", type(sample)) @@ -1620,42 +1583,7 @@ class SampleList(list): #### For extra attribute columns; currently only used by two human datasets - Zach if this_trait and this_trait.db and this_trait.db.type == 'ProbeSet': - if len(attribute_ids) > 0: - - #ZS: Get StrainId value for the next query - cursor.execute("""SELECT Strain.Id - FROM Strain, StrainXRef, InbredSetd - WHERE Strain.Name = '%s' and - StrainXRef.StrainId = Strain.Id and - InbredSet.Id = StrainXRef.InbredSetId and - InbredSet.Name = '%s'""" % (sampleName, fd.RISet)) - - sample_id = cursor.fetchone()[0] - - attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column). - for attribute_id in attribute_ids: - - #ZS: Add extra case attribute values (if any) - cursor.execute("""SELECT Value - FROM CaseAttributeXRef - WHERE ProbeSetFreezeId = '%s' AND - StrainId = '%s' AND - CaseAttributeId = '%s' - group by CaseAttributeXRef.CaseAttributeId""" % (this_trait.db.id, sample_id, str(attribute_id))) - - attributeValue = cursor.fetchone()[0] #Trait-specific attributes, if any - - #ZS: If it's an int, turn it into one for sorting (for example, 101 would be lower than 80 if they're strings instead of ints) - try: - attributeValue = int(attributeValue) - except: - pass - - span_Id = samples+"_attribute"+str(attr_counter)+"_sample"+str(i+1) - attr_container = HT.Span(attributeValue, Id=span_Id) - attr_className = str(attributeValue) + " " + className - table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) - attr_counter += 1 + self.get_extra_attribute_values(attribute_ids, this_trait, sample_name) self.append(sample) #table_body.append(table_row) @@ -1679,3 +1607,99 @@ class SampleList(list): sample.outlier = True else: sample.outlier = False + + def calc_attributes(self): + """Finds which extra attributes apply to this dataset""" + + + #ZS: Id and name values for this trait's extra attributes + self.cursor.execute('''SELECT CaseAttribute.Id, CaseAttribute.Name + FROM CaseAttribute, CaseAttributeXRef + WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND + CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId + group by CaseAttributeXRef.CaseAttributeId''', + (str(this_trait.db.id),)) + + #self.attributes = {key, value in self.cursor.fetchall()} + #self.attributes = OrderedDict(self.attributes.iteritems()) + + self.attributes = {} + for key, value in self.cursor.fetchall(): + self.attributes[key] = Bunch() + self.attributes[key].name = value + + self.cursor.execute('''SELECT DISTINCT CaseAttributeXRef.Value + FROM CaseAttribute, CaseAttributeXRef + WHERE CaseAttribute.Name = %s AND + CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id''', (value,)) + + self.attributes[key].distinct_values = self.cursor.fetchall() + + + try: + + exclude_menu = HT.Select(name="exclude_menu") + dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) + + for attribute in self.cursor.fetchall(): + attribute_ids.append(attribute[0]) + attribute_names.append(attribute[1]) + for this_attr_name in attribute_names: + exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) + self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value + FROM CaseAttribute, CaseAttributeXRef + WHERE CaseAttribute.Name = '%s' AND + CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""" % (this_attr_name)) + try: + distinct_values = self.cursor.fetchall() + attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus + attr_value_menu = HT.Select(name=this_attr_name) + attr_value_menu.append(("None", "show_all")) + for value in distinct_values: + attr_value_menu.append((str(value[0]), value[0])) + attr_value_menu_div.append(attr_value_menu) + dropdown_menus.append(attr_value_menu_div) + except: + pass + except: + pass + + + def get_extra_attribute_values(self): + + if len(attribute_ids) > 0: + + #ZS: Get StrainId value for the next query + cursor.execute("""SELECT Strain.Id + FROM Strain, StrainXRef, InbredSetd + WHERE Strain.Name = '%s' and + StrainXRef.StrainId = Strain.Id and + InbredSet.Id = StrainXRef.InbredSetId and + InbredSet.Name = '%s'""" % (sampleName, fd.RISet)) + + sample_id = cursor.fetchone()[0] + + attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column). + for attribute_id in attribute_ids: + + #ZS: Add extra case attribute values (if any) + cursor.execute("""SELECT Value + FROM CaseAttributeXRef + WHERE ProbeSetFreezeId = '%s' AND + StrainId = '%s' AND + CaseAttributeId = '%s' + group by CaseAttributeXRef.CaseAttributeId""" % (this_trait.db.id, sample_id, str(attribute_id))) + + attributeValue = cursor.fetchone()[0] #Trait-specific attributes, if any + + #ZS: If it's an int, turn it into one for sorting (for example, 101 would be lower than 80 if they're strings instead of ints) + try: + attributeValue = int(attributeValue) + except ValueError: + pass + + span_Id = samples+"_attribute"+str(attr_counter)+"_sample"+str(i+1) + attr_container = HT.Span(attributeValue, Id=span_Id) + attr_className = str(attributeValue) + " " + className + table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) + attr_counter += 1 -- cgit 1.4.1 From 45fb8b4961e1dc8251502f04cb94a4fcf1848f83 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Thu, 27 Sep 2012 17:40:16 -0500 Subject: Worked on getting attributes in the SampleList object to display data properly, changed SampleList from an object list to object --- wqflask/base/webqtlTrait.py | 16 +- wqflask/utility/__init__.py | 14 +- wqflask/wqflask/__init__.py | 3 + wqflask/wqflask/show_trait/DataEditingPage.py | 192 ++++++++++----------- .../wqflask/templates/trait_data_and_analysis.html | 4 +- 5 files changed, 113 insertions(+), 116 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py index efbc1464..d6d537b7 100755 --- a/wqflask/base/webqtlTrait.py +++ b/wqflask/base/webqtlTrait.py @@ -359,14 +359,14 @@ class webqtlTrait: #else: # pass - def keys(self): - return self.__dict__.keys() - - def has_key(self, key): - return self.__dict__.has_key(key) - - def items(self): - return self.__dict__.items() + #def keys(self): + # return self.__dict__.keys() + # + #def has_key(self, key): + # return self.__dict__.has_key(key) + # + #def items(self): + # return self.__dict__.items() def retrieveInfo(self, QTL = None): assert self.db and self.cursor diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index 206d0d1c..d0e4a3fa 100755 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -1,12 +1,12 @@ +from pprint import pformat as pf + + class Bunch(object): - """Make the configuration a little cleaner""" - def __init__(self, config_string = "", **kw): - if config_string: - td = yaml.load(config_string) - self.__dict__.update(td) - else: + """Like a dictionary but using object notation""" + def __init__(self, **kw): self.__dict__ = kw def __repr__(self): - return yaml.dump(self.__dict__, default_flow_style=False) + return pf(self.__dict__) + diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index a7492e77..ff018fdc 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -3,6 +3,8 @@ from __future__ import absolute_import, division, print_function import sys print("sys.path is:", sys.path) +import jinja2 + from flask import Flask from utility import formatting @@ -14,6 +16,7 @@ app.config.from_object('cfg.default_settings') app.config.from_envvar('WQFLASK_SETTINGS') app.jinja_env.globals.update( + undefined = jinja2.StrictUndefined, numify = formatting.numify ) diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index e431fd76..24a37926 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -1466,43 +1466,23 @@ class DataEditingPage(templatePage): if fd.genotype.type == "riset": all_samples_ordered = fd.f1list + fd.samplelist else: - all_samples_ordered = fd.f1list + fd.parlist + fd.samplelist - - #ZS: Id values for this trait's extra attributes; - #used to create "Exclude" dropdown and query for attribute values and create - self.cursor.execute("""SELECT CaseAttribute.Id, CaseAttribute.Name - FROM CaseAttribute, CaseAttributeXRef - WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND - CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId - group by CaseAttributeXRef.CaseAttributeId""", - (str(this_trait.db.id),)) - - - - for this_attr_name in attribute_names: - # Todo: Needs testing still! - self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value - FROM CaseAttribute, CaseAttributeXRef - WHERE CaseAttribute.Name = %s AND - CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""", - (this_attr_name,)) - - distinct_values = self.cursor.fetchall() + all_samples_ordered = fd.parlist + fd.f1list + fd.samplelist this_trait_samples = set(this_trait.data.keys()) primary_sample_names = all_samples_ordered - print("primary_samplelist is:", pf(primary_sample_names)) + print("-*- primary_samplelist is:", pf(primary_sample_names)) primary_samples = SampleList(self.cursor, fd=fd, variance_data_page=variance_data_page, sample_names=primary_sample_names, this_trait=this_trait, - samples='primary', + sample_group_type='primary', header="%s Only" % (fd.RISet)) - + + print("primary_samples.attributes:", pf(primary_samples.attributes)) other_sample_names = [] for sample in this_trait.data.keys(): @@ -1515,15 +1495,15 @@ class DataEditingPage(templatePage): unappended_par_f1 = fd.f1list + fd.parlist par_f1_samples = ["_2nd_" + sample for sample in unappended_par_f1] - other_samples.sort() #Sort other samples - other_samples = par_f1_samples + other_samples + other_sample_names.sort() #Sort other samples + other_sample_names = par_f1_samples + other_sample_names other_samples = SampleList(self.cursor, fd=fd, variance_data_page=variance_data_page, sample_names=other_sample_names, this_trait=this_trait, - samples='other', + sample_group_type='other', header="Non-%s" % (fd.RISet)) self.sample_groups = (primary_samples, other_samples) @@ -1531,36 +1511,39 @@ class DataEditingPage(templatePage): self.sample_groups = (primary_samples,) #TODO: Figure out why this if statement is written this way - Zach - if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0])) - or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))): - print("hjs") - fd.allsamplelist = all_samples_ordered - - - + #if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0])) + # or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))): + # print("hjs") + fd.allsamplelist = all_samples_ordered -class SampleList(list): +class SampleList(object): def __init__(self, cursor, fd, variance_data_page, sample_names, this_trait, - samples, + sample_group_type, header): + self.cursor = cursor + self.fd = fd + self.this_trait = this_trait + self.sample_group_type = sample_group_type # primary or other self.header = header - - + + self.sample_list = [] # The actual list self.calc_attributes() + + print("camera: attributes are:", pf(self.attributes)) for counter, sample_name in enumerate(sample_names, 1): sample_name = sample_name.replace("_2nd_", "") #ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table) try: - sample = this_trait.data[sample_name] + sample = self.this_trait.data[sample_name] except KeyError: print("No sample %s, let's create it now" % sample_name) sample = webqtlCaseData.webqtlCaseData(sample_name) @@ -1569,37 +1552,37 @@ class SampleList(list): #if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'): # sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") sample.extra_info = {} - if fd.RISet == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'): + if self.fd.RISet == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'): sample.extra_info['url'] = "/mouseCross.html#AXB/BXA" sample.extra_info['css_class'] = "fs12" - - print("zyt - sampleNameOrig:", sampleNameOrig) + print(" type of sample:", type(sample)) - if samples == 'primary': + if sample_group_type == 'primary': sample.this_id = "Primary_" + str(counter) else: sample.this_id = "Other_" + str(counter) #### For extra attribute columns; currently only used by two human datasets - Zach - if this_trait and this_trait.db and this_trait.db.type == 'ProbeSet': - self.get_extra_attribute_values(attribute_ids, this_trait, sample_name) - self.append(sample) - #table_body.append(table_row) + if self.this_trait and self.this_trait.db and self.this_trait.db.type == 'ProbeSet': + self.get_extra_attribute_values(sample_name) + self.sample_list.append(sample) self.do_outliers() #do_outliers(the_samples) - print("*the_samples are [%i]: %s" % (len(self), pf(self))) - for sample in self: + print("*the_samples are [%i]: %s" % (len(self.sample_list), pf(self.sample_list))) + for sample in self.sample_list: print("apple:", type(sample), sample) #return the_samples + def __repr__(self): + return " --> %s" % (pf(self.__dict__)) def do_outliers(self): - values = [sample.value for sample in self if sample.value != None] + values = [sample.value for sample in self.sample_list if sample.value != None] upper_bound, lower_bound = Plot.find_outliers(values) - for sample in self: + for sample in self.sample_list: if sample.value: if upper_bound and sample.value > upper_bound: sample.outlier = True @@ -1608,23 +1591,24 @@ class SampleList(list): else: sample.outlier = False + def calc_attributes(self): """Finds which extra attributes apply to this dataset""" - #ZS: Id and name values for this trait's extra attributes self.cursor.execute('''SELECT CaseAttribute.Id, CaseAttribute.Name FROM CaseAttribute, CaseAttributeXRef WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId group by CaseAttributeXRef.CaseAttributeId''', - (str(this_trait.db.id),)) + (str(self.this_trait.db.id),)) #self.attributes = {key, value in self.cursor.fetchall()} #self.attributes = OrderedDict(self.attributes.iteritems()) self.attributes = {} for key, value in self.cursor.fetchall(): + print("radish: %s - %s" % (key, value)) self.attributes[key] = Bunch() self.attributes[key].name = value @@ -1633,64 +1617,65 @@ class SampleList(list): WHERE CaseAttribute.Name = %s AND CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id''', (value,)) - self.attributes[key].distinct_values = self.cursor.fetchall() - - - try: - - exclude_menu = HT.Select(name="exclude_menu") - dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) - - for attribute in self.cursor.fetchall(): - attribute_ids.append(attribute[0]) - attribute_names.append(attribute[1]) - for this_attr_name in attribute_names: - exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) - self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value - FROM CaseAttribute, CaseAttributeXRef - WHERE CaseAttribute.Name = '%s' AND - CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""" % (this_attr_name)) - try: - distinct_values = self.cursor.fetchall() - attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus - attr_value_menu = HT.Select(name=this_attr_name) - attr_value_menu.append(("None", "show_all")) - for value in distinct_values: - attr_value_menu.append((str(value[0]), value[0])) - attr_value_menu_div.append(attr_value_menu) - dropdown_menus.append(attr_value_menu_div) - except: - pass - except: - pass + self.attributes[key].distinct_values = [item[0] for item in self.cursor.fetchall()] + self.attributes[key].distinct_values.sort(key=natural_sort_key) + + + #try: + # + # exclude_menu = HT.Select(name="exclude_menu") + # dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) + # + # for attribute in self.cursor.fetchall(): + # attribute_ids.append(attribute[0]) + # attribute_names.append(attribute[1]) + # for this_attr_name in attribute_names: + # exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) + # self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value + # FROM CaseAttribute, CaseAttributeXRef + # WHERE CaseAttribute.Name = '%s' AND + # CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""" % (this_attr_name)) + # try: + # distinct_values = self.cursor.fetchall() + # attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus + # attr_value_menu = HT.Select(name=this_attr_name) + # attr_value_menu.append(("None", "show_all")) + # for value in distinct_values: + # attr_value_menu.append((str(value[0]), value[0])) + # attr_value_menu_div.append(attr_value_menu) + # dropdown_menus.append(attr_value_menu_div) + # except: + # pass + #except: + # pass - def get_extra_attribute_values(self): + def get_extra_attribute_values(self, sample_name): - if len(attribute_ids) > 0: + if len(self.attributes) > 0: #ZS: Get StrainId value for the next query - cursor.execute("""SELECT Strain.Id - FROM Strain, StrainXRef, InbredSetd - WHERE Strain.Name = '%s' and + self.cursor.execute("""SELECT Strain.Id + FROM Strain, StrainXRef, InbredSet + WHERE Strain.Name = %s and StrainXRef.StrainId = Strain.Id and InbredSet.Id = StrainXRef.InbredSetId and - InbredSet.Name = '%s'""" % (sampleName, fd.RISet)) + InbredSet.Name = %s""", (sample_name, self.fd.RISet)) - sample_id = cursor.fetchone()[0] + sample_id = self.cursor.fetchone()[0] attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column). - for attribute_id in attribute_ids: + for attribute_id in self.attributes.keys(): #ZS: Add extra case attribute values (if any) - cursor.execute("""SELECT Value + self.cursor.execute("""SELECT Value FROM CaseAttributeXRef WHERE ProbeSetFreezeId = '%s' AND StrainId = '%s' AND CaseAttributeId = '%s' - group by CaseAttributeXRef.CaseAttributeId""" % (this_trait.db.id, sample_id, str(attribute_id))) + group by CaseAttributeXRef.CaseAttributeId""" % (self.this_trait.db.id, sample_id, str(attribute_id))) - attributeValue = cursor.fetchone()[0] #Trait-specific attributes, if any + attributeValue = self.cursor.fetchone()[0] #Trait-specific attributes, if any #ZS: If it's an int, turn it into one for sorting (for example, 101 would be lower than 80 if they're strings instead of ints) try: @@ -1698,8 +1683,17 @@ class SampleList(list): except ValueError: pass - span_Id = samples+"_attribute"+str(attr_counter)+"_sample"+str(i+1) - attr_container = HT.Span(attributeValue, Id=span_Id) - attr_className = str(attributeValue) + " " + className - table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) + #span_Id = samples+"_attribute"+str(attr_counter)+"_sample"+str(i+1) + #attr_container = HT.Span(attributeValue, Id=span_Id) + #attr_className = str(attributeValue) + " " + className + #table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) attr_counter += 1 + + +def natural_sort_key(x): + """Get expected results when using as a key for sort - ints or strings are sorted properly""" + try: + x = int(x) + except ValueError: + pass + return x \ No newline at end of file diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html index 7cfb7916..6a5a4a80 100644 --- a/wqflask/wqflask/templates/trait_data_and_analysis.html +++ b/wqflask/wqflask/templates/trait_data_and_analysis.html @@ -1249,7 +1249,7 @@

{{ sample_type.header }}

-
+
@@ -1265,7 +1265,7 @@ - {% for sample in sample_type %} + {% for sample in sample_type.sample_list %}
SE
{{ loop.index }} -- cgit 1.4.1