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 __init__(self, fd):
templatePage.__init__(self, fd)
self.initializeDisplayParameters(fd)
if not fd.genotype:
fd.readGenotype()
if fd.allstrainlist:
mdpchoice = fd.formdata.getvalue('MDPChoice')
if mdpchoice == "1":
strainlist = fd.f1list + fd.strainlist
elif mdpchoice == "2":
strainlist = []
strainlist2 = fd.f1list + fd.strainlist
for strain in fd.allstrainlist:
if strain not in strainlist2:
strainlist.append(strain)
#So called MDP Panel
if strainlist:
strainlist = fd.f1list+fd.parlist+strainlist
else:
strainlist = fd.allstrainlist
fd.readData(fd.allstrainlist)
else:
mdpchoice = None
strainlist = fd.strainlist
fd.readData()
#if fd.allstrainlist:
# fd.readData(fd.allstrainlist)
# strainlist = fd.allstrainlist
#else:
# fd.readData()
# strainlist = fd.strainlist
if not self.openMysql():
return
isSampleCorr = 0 #XZ: initial value is false
isTissueCorr = 0 #XZ: initial value is false
#Javascript functions (showCorrelationPlot2, showTissueCorrPlot) have made sure the correlation type is either sample correlation or tissue correlation.
if (self.database and (self.ProbeSetID != 'none')):
isSampleCorr = 1
elif (self.X_geneSymbol and self.Y_geneSymbol):
isTissueCorr = 1
else:
heading = "Correlation Type Error"
detail = ["For the input parameters, GN can not recognize the correlation type is sample correlation or tissue correlation."]
self.error(heading=heading,detail=detail)
return
TD_LR = HT.TD(colspan=2,height=200,width="100%",bgColor='#eeeeee', align="left", wrap="off")
dataX=[]
dataY=[]
dataZ=[] # shortname
fullTissueName=[]
if isTissueCorr:
dataX, dataY, xlabel, ylabel, dataZ, fullTissueName = self.getTissueLabelsValues(X_geneSymbol=self.X_geneSymbol, Y_geneSymbol=self.Y_geneSymbol, TissueProbeSetFreezeId=self.TissueProbeSetFreezeId)
plotHeading = HT.Paragraph('Tissue Correlation Scatterplot')
plotHeading.__setattr__("class","title")
if self.xAxisLabel == '':
self.xAxisLabel = xlabel
if self.yAxisLabel == '':
self.yAxisLabel = ylabel
if isSampleCorr:
plotHeading = HT.Paragraph('Sample Correlation Scatterplot')
plotHeading.__setattr__("class","title")
#XZ: retrieve trait 1 info, Y axis
trait1_data = [] #trait 1 data
trait1Url = ''
try:
Trait1 = webqtlTrait(db=self.database, name=self.ProbeSetID, cellid=self.CellID, cursor=self.cursor)
Trait1.retrieveInfo()
Trait1.retrieveData()
except:
heading = "Retrieve Data"
detail = ["The database you just requested has not been established yet."]
self.error(heading=heading,detail=detail)
return
trait1_data = Trait1.exportData(strainlist)
if Trait1.db.type == 'Publish' and Trait1.confidential:
trait1Url = Trait1.genHTML(dispFromDatabase=1, privilege=self.privilege, userName=self.userName, authorized_users=Trait1.authorized_users)
else:
trait1Url = Trait1.genHTML(dispFromDatabase=1)
if self.yAxisLabel == '':
self.yAxisLabel= '%s : %s' % (Trait1.db.shortname, Trait1.name)
if Trait1.cellid:
self.yAxisLabel += ' : ' + Trait1.cellid
#XZ, retrieve trait 2 info, X axis
traitdata2 = [] #trait 2 data
_vals = [] #trait 2 data
trait2Url = ''
if ( self.database2 and (self.ProbeSetID2 != 'none') ):
try:
Trait2 = webqtlTrait(db=self.database2, name=self.ProbeSetID2, cellid=self.CellID2, cursor=self.cursor)
Trait2.retrieveInfo()
Trait2.retrieveData()
except:
heading = "Retrieve Data"
detail = ["The database you just requested has not been established yet."]
self.error(heading=heading,detail=detail)
return
if Trait2.db.type == 'Publish' and Trait2.confidential:
trait2Url = Trait2.genHTML(dispFromDatabase=1, privilege=self.privilege, userName=self.userName, authorized_users=Trait2.authorized_users)
else:
trait2Url = Trait2.genHTML(dispFromDatabase=1)
traitdata2 = Trait2.exportData(strainlist)
_vals = traitdata2[:]
if self.xAxisLabel == '':
self.xAxisLabel = '%s : %s' % (Trait2.db.shortname, Trait2.name)
if Trait2.cellid:
self.xAxisLabel += ' : ' + Trait2.cellid
else:
for item in strainlist:
if fd.allTraitData.has_key(item):
_vals.append(fd.allTraitData[item].val)
else:
_vals.append(None)
if self.xAxisLabel == '':
if fd.identification:
self.xAxisLabel = fd.identification
else:
self.xAxisLabel = "User Input Data"
try:
Trait2 = webqtlTrait(fullname=fd.formdata.getvalue('fullname'), cursor=self.cursor)
trait2Url = Trait2.genHTML(dispFromDatabase=1)
except:
trait2Url = self.xAxisLabel
if (_vals and trait1_data):
if len(_vals) != len(trait1_data):
errors = HT.Blockquote(HT.Font('Error: ',color='red'),HT.Font('The number of traits are inconsistent, Program quit',color='black'))
errors.__setattr__("class","subtitle")
TD_LR.append(errors)
self.dict['body'] = str(TD_LR)
return
for i in range(len(_vals)):
if _vals[i]!= None and trait1_data[i]!= None:
dataX.append(_vals[i])
dataY.append(trait1_data[i])
strainName = strainlist[i]
if self.showstrains:
dataZ.append(webqtlUtil.genShortStrainName(RISet=fd.RISet, input_strainName=strainName))
else:
heading = "Correlation Plot"
detail = ['Empty Dataset for sample correlation, please check your data.']
self.error(heading=heading,detail=detail)
return
#XZ: We have gotten all data for both traits.
if len(dataX) >= self.corrMinInformative:
if self.rankOrder == 0:
rankPrimary = 0
rankSecondary = 1
else:
rankPrimary = 1
rankSecondary = 0
lineColor = self.setLineColor();
symbolColor = self.setSymbolColor();
idColor = self.setIdColor();
c = pid.PILCanvas(size=(self.plotSize, self.plotSize*0.90))
data_coordinate = Plot.plotXY(canvas=c, dataX=dataX, dataY=dataY, rank=rankPrimary, dataLabel = dataZ, labelColor=pid.black, lineSize=self.lineSize, lineColor=lineColor, idColor=idColor, idFont=self.idFont, idSize=self.idSize, symbolColor=symbolColor, symbolType=self.symbol, filled=self.filled, symbolSize=self.symbolSize, XLabel=self.xAxisLabel, connectdot=0, YLabel=self.yAxisLabel, title='', fitcurve=self.showline, displayR =1, offset= (90, self.plotSize/20, self.plotSize/10, 90), showLabel = self.showIdentifiers)
if rankPrimary == 1:
dataXlabel, dataYlabel = webqtlUtil.calRank(xVals=dataX, yVals=dataY, N=len(dataX))
else:
dataXlabel, dataYlabel = dataX, dataY
gifmap1 = HT.Map(name='CorrelationPlotImageMap1')
for i, item in enumerate(data_coordinate):
one_rect_coordinate = "%d, %d, %d, %d" % (item[0] - 5, item[1] - 5, item[0] + 5, item[1] + 5)
if isTissueCorr:
one_rect_title = "%s (%s, %s)" % (fullTissueName[i], dataXlabel[i], dataYlabel[i])
else:
one_rect_title = "%s (%s, %s)" % (dataZ[i], dataXlabel[i], dataYlabel[i])
gifmap1.areas.append(HT.Area(shape='rect',coords=one_rect_coordinate, title=one_rect_title) )
filename= webqtlUtil.genRandStr("XY_")
c.save(webqtlConfig.IMGDIR+filename, format='gif')
img1=HT.Image('/image/'+filename+'.gif',border=0, usemap='#CorrelationPlotImageMap1')
mainForm_1 = HT.Form( cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet, 'ProbeSetID2':'_', 'database2':'_', 'CellID2':'_', 'allstrainlist':string.join(fd.strainlist, " "), 'traitList': fd.formdata.getvalue("traitList")}
if fd.incparentsf1:
hddn['incparentsf1'] = 'ON'
for key in hddn.keys():
mainForm_1.append(HT.Input(name=key, value=hddn[key], type='hidden'))
if isSampleCorr:
mainForm_1.append(HT.P(), HT.Blockquote(HT.Strong('X axis:'),HT.Blockquote(trait2Url),HT.Strong('Y axis:'),HT.Blockquote(trait1Url), style='width: %spx;' % self.plotSize, wrap="hard"))
graphForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), name='MDP_Form',submit=HT.Input(type='hidden'))
graph_hddn = self.setHiddenParameters(fd, rankPrimary)
webqtlUtil.exportData(graph_hddn, fd.allTraitData) #XZ: This is necessary to replot with different groups of strains
for key in graph_hddn.keys():
graphForm.append(HT.Input(name=key, value=graph_hddn[key], type='hidden'))
options = self.createOptionsMenu(fd, mdpchoice)
if (self.showOptions == '0'):
showOptionsButton = HT.Input(type='button' ,name='optionsButton',value='Hide Options', onClick="showHideOptions();", Class="button")
else:
showOptionsButton = HT.Input(type='button' ,name='optionsButton',value='Show Options', onClick="showHideOptions();", Class="button")
# updated by NL: 12-07-2011 add variables for tissue abbreviation page
if isTissueCorr:
graphForm.append(HT.Input(name='shortTissueName', value='', type='hidden'))
graphForm.append(HT.Input(name='fullTissueName', value='', type='hidden'))
shortTissueNameStr=string.join(dataZ, ",")
fullTissueNameStr=string.join(fullTissueName, ",")
tissueAbbrButton=HT.Input(type='button' ,name='tissueAbbrButton',value='Show Abbreviations', onClick="showTissueAbbr('MDP_Form','%s','%s')" % (shortTissueNameStr,fullTissueNameStr), Class="button")
graphForm.append(showOptionsButton,' ',tissueAbbrButton, HT.BR(), HT.BR())
else:
graphForm.append(showOptionsButton, HT.BR(), HT.BR())
graphForm.append(options, HT.BR())
graphForm.append(HT.HR(), HT.BR(), HT.P())
TD_LR.append(plotHeading, HT.BR(),graphForm, HT.BR(), gifmap1, HT.P(), img1, HT.P(), mainForm_1)
TD_LR.append(HT.BR(), HT.HR(color="grey", size=5, width="100%"))
c = pid.PILCanvas(size=(self.plotSize, self.plotSize*0.90))
data_coordinate = Plot.plotXY(canvas=c, dataX=dataX, dataY=dataY, rank=rankSecondary, dataLabel = dataZ, labelColor=pid.black,lineColor=lineColor, lineSize=self.lineSize, idColor=idColor, idFont=self.idFont, idSize=self.idSize, symbolColor=symbolColor, symbolType=self.symbol, filled=self.filled, symbolSize=self.symbolSize, XLabel=self.xAxisLabel, connectdot=0, YLabel=self.yAxisLabel,title='', fitcurve=self.showline, displayR =1, offset= (90, self.plotSize/20, self.plotSize/10, 90), showLabel = self.showIdentifiers)
if rankSecondary == 1:
dataXlabel, dataYlabel = webqtlUtil.calRank(xVals=dataX, yVals=dataY, N=len(dataX))
else:
dataXlabel, dataYlabel = dataX, dataY
gifmap2 = HT.Map(name='CorrelationPlotImageMap2')
for i, item in enumerate(data_coordinate):
one_rect_coordinate = "%d, %d, %d, %d" % (item[0] - 6, item[1] - 6, item[0] + 6, item[1] + 6)
if isTissueCorr:
one_rect_title = "%s (%s, %s)" % (fullTissueName[i], dataXlabel[i], dataYlabel[i])
else:
one_rect_title = "%s (%s, %s)" % (dataZ[i], dataXlabel[i], dataYlabel[i])
gifmap2.areas.append(HT.Area(shape='rect',coords=one_rect_coordinate, title=one_rect_title) )
filename= webqtlUtil.genRandStr("XY_")
c.save(webqtlConfig.IMGDIR+filename, format='gif')
img2=HT.Image('/image/'+filename+'.gif',border=0, usemap='#CorrelationPlotImageMap2')
mainForm_2 = HT.Form( cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase2', submit=HT.Input(type='hidden'))
hddn = {'FormID':'showDatabase2','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet, 'ProbeSetID2':'_', 'database2':'_', 'CellID2':'_', 'allstrainlist':string.join(fd.strainlist, " "), 'traitList': fd.formdata.getvalue("traitList")}
if fd.incparentsf1:
hddn['incparentsf1'] = 'ON'
for key in hddn.keys():
mainForm_2.append(HT.Input(name=key, value=hddn[key], type='hidden'))
if isSampleCorr:
mainForm_2.append(HT.P(), HT.Blockquote(HT.Strong('X axis:'),HT.Blockquote(trait2Url),HT.Strong('Y axis:'),HT.Blockquote(trait1Url), style='width:%spx;' % self.plotSize))
TD_LR.append(HT.BR(), HT.P())
TD_LR.append('\n', gifmap2, HT.P(), HT.P(), img2, HT.P(), mainForm_2)
self.dict['body'] = str(TD_LR)
else:
heading = "Correlation Plot"
detail = ['Fewer than %d strain data were entered for %s data set. No statitical analysis has been attempted.' % (self.corrMinInformative, fd.RISet)]
self.error(heading=heading,detail=detail)
return
def __init__(self, fd):
templatePage.__init__(self, fd)
self.initializeDisplayParameters(fd)
if not fd.genotype:
fd.readGenotype()
mdpchoice = None
strainlist = fd.strainlist
fd.readData()
if not self.openMysql():
return
isSampleCorr = 1
isTissueCorr = 0
TD_LR = HT.TD(colspan=2, height=200, width="100%", bgColor="#eeeeee", align="left", wrap="off")
dataX = []
dataY = []
dataZ = [] # shortname
fullTissueName = []
xlabel = ""
ylabel = ""
if isSampleCorr:
plotHeading = HT.Paragraph("Sample Correlation Scatterplot")
plotHeading.__setattr__("class", "title")
# XZ: retrieve trait 1 info, Y axis
trait1_data = [] # trait 1 data
trait1Url = ""
try:
Trait1 = webqtlTrait(db=self.database, name=self.ProbeSetID, cellid=self.CellID, cursor=self.cursor)
Trait1.retrieveInfo()
Trait1.retrieveData()
except:
heading = "Retrieve Data"
detail = ["The database you just requested has not been established yet."]
self.error(heading=heading, detail=detail)
return
trait1_data = Trait1.exportData(strainlist)
trait1Url = Trait1.genHTML(dispFromDatabase=1)
ylabel = "%s : %s" % (Trait1.db.shortname, Trait1.name)
if Trait1.cellid:
ylabel += " : " + Trait1.cellid
# XZ, retrieve trait 2 info, X axis
trait2_data = [] # trait 2 data
trait2Url = ""
try:
Trait2 = webqtlTrait(db=self.database2, name=self.ProbeSetID2, cellid=self.CellID2, cursor=self.cursor)
Trait2.retrieveInfo()
Trait2.retrieveData()
except:
heading = "Retrieve Data"
detail = ["The database you just requested has not been established yet."]
self.error(heading=heading, detail=detail)
return
trait2_data = Trait2.exportData(strainlist)
trait2Url = Trait2.genHTML(dispFromDatabase=1)
xlabel = "%s : %s" % (Trait2.db.shortname, Trait2.name)
if Trait2.cellid:
xlabel += " : " + Trait2.cellid
for strain in Trait1.data.keys():
if Trait2.data.has_key(strain):
dataX.append(Trait2.data[strain].val)
dataY.append(Trait1.data[strain].val)
if self.showstrains:
dataZ.append(webqtlUtil.genShortStrainName(RISet=fd.RISet, input_strainName=strain))
# XZ: We have gotten all data for both traits.
if len(dataX) >= self.corrMinInformative:
if self.rankOrder == 0:
rankPrimary = 0
rankSecondary = 1
else:
rankPrimary = 1
rankSecondary = 0
lineColor = self.setLineColor()
symbolColor = self.setSymbolColor()
idColor = self.setIdColor()
c = pid.PILCanvas(size=(self.plotSize, self.plotSize * 0.90))
data_coordinate = Plot.plotXY(
canvas=c,
dataX=dataX,
dataY=dataY,
rank=rankPrimary,
dataLabel=dataZ,
labelColor=pid.black,
lineSize=self.lineSize,
lineColor=lineColor,
idColor=idColor,
idFont=self.idFont,
idSize=self.idSize,
symbolColor=symbolColor,
symbolType=self.symbol,
filled=self.filled,
symbolSize=self.symbolSize,
XLabel=xlabel,
connectdot=0,
YLabel=ylabel,
title="",
fitcurve=self.showline,
displayR=1,
offset=(90, self.plotSize / 20, self.plotSize / 10, 90),
showLabel=self.showIdentifiers,
)
if rankPrimary == 1:
dataXlabel, dataYlabel = webqtlUtil.calRank(xVals=dataX, yVals=dataY, N=len(dataX))
else:
dataXlabel, dataYlabel = dataX, dataY
gifmap1 = HT.Map(name="CorrelationPlotImageMap1")
for i, item in enumerate(data_coordinate):
one_rect_coordinate = "%d, %d, %d, %d" % (item[0] - 5, item[1] - 5, item[0] + 5, item[1] + 5)
if isTissueCorr:
one_rect_title = "%s (%s, %s)" % (fullTissueName[i], dataXlabel[i], dataYlabel[i])
else:
one_rect_title = "%s (%s, %s)" % (dataZ[i], dataXlabel[i], dataYlabel[i])
gifmap1.areas.append(HT.Area(shape="rect", coords=one_rect_coordinate, title=one_rect_title))
filename = webqtlUtil.genRandStr("XY_")
c.save(webqtlConfig.IMGDIR + filename, format="gif")
img1 = HT.Image("/image/" + filename + ".gif", border=0, usemap="#CorrelationPlotImageMap1")
mainForm_1 = HT.Form(
cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
enctype="multipart/form-data",
name="showDatabase",
submit=HT.Input(type="hidden"),
)
hddn = {
"FormID": "showDatabase",
"ProbeSetID": "_",
"database": "_",
"CellID": "_",
"RISet": fd.RISet,
"ProbeSetID2": "_",
"database2": "_",
"CellID2": "_",
"allstrainlist": string.join(fd.strainlist, " "),
"traitList": fd.formdata.getvalue("traitList"),
}
if fd.incparentsf1:
hddn["incparentsf1"] = "ON"
for key in hddn.keys():
mainForm_1.append(HT.Input(name=key, value=hddn[key], type="hidden"))
if isSampleCorr:
mainForm_1.append(
HT.P(),
HT.Blockquote(
HT.Strong("X axis:"),
HT.Blockquote(trait2Url),
HT.Strong("Y axis:"),
HT.Blockquote(trait1Url),
style="width: %spx;" % self.plotSize,
wrap="hard",
),
)
graphForm = HT.Form(
cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
name="MDP_Form",
submit=HT.Input(type="hidden"),
)
graph_hddn = self.setHiddenParameters(fd, rankPrimary)
webqtlUtil.exportData(
graph_hddn, fd.allTraitData
) # XZ: This is necessary to replot with different groups of strains
for key in graph_hddn.keys():
graphForm.append(HT.Input(name=key, value=graph_hddn[key], type="hidden"))
options = self.createOptionsMenu(fd, mdpchoice)
if self.showOptions == "0":
showOptionsButton = HT.Input(
type="button",
name="optionsButton",
value="Hide Options",
onClick="showHideOptions();",
Class="button",
)
else:
showOptionsButton = HT.Input(
type="button",
name="optionsButton",
value="Show Options",
onClick="showHideOptions();",
Class="button",
)
# updated by NL: 12-07-2011 add variables for tissue abbreviation page
if isTissueCorr:
graphForm.append(HT.Input(name="shortTissueName", value="", type="hidden"))
graphForm.append(HT.Input(name="fullTissueName", value="", type="hidden"))
shortTissueNameStr = string.join(dataZ, ",")
fullTissueNameStr = string.join(fullTissueName, ",")
tissueAbbrButton = HT.Input(
type="button",
name="tissueAbbrButton",
value="Show Abbreviations",
onClick="showTissueAbbr('MDP_Form','%s','%s')" % (shortTissueNameStr, fullTissueNameStr),
Class="button",
)
graphForm.append(showOptionsButton, " ", tissueAbbrButton, HT.BR(), HT.BR())
else:
graphForm.append(showOptionsButton, HT.BR(), HT.BR())
graphForm.append(options, HT.BR())
graphForm.append(HT.HR(), HT.BR(), HT.P())
TD_LR.append(plotHeading, HT.BR(), graphForm, HT.BR(), gifmap1, HT.P(), img1, HT.P(), mainForm_1)
TD_LR.append(HT.BR(), HT.HR(color="grey", size=5, width="100%"))
c = pid.PILCanvas(size=(self.plotSize, self.plotSize * 0.90))
data_coordinate = Plot.plotXY(
canvas=c,
dataX=dataX,
dataY=dataY,
rank=rankSecondary,
dataLabel=dataZ,
labelColor=pid.black,
lineColor=lineColor,
lineSize=self.lineSize,
idColor=idColor,
idFont=self.idFont,
idSize=self.idSize,
symbolColor=symbolColor,
symbolType=self.symbol,
filled=self.filled,
symbolSize=self.symbolSize,
XLabel=xlabel,
connectdot=0,
YLabel=ylabel,
title="",
fitcurve=self.showline,
displayR=1,
offset=(90, self.plotSize / 20, self.plotSize / 10, 90),
showLabel=self.showIdentifiers,
)
if rankSecondary == 1:
dataXlabel, dataYlabel = webqtlUtil.calRank(xVals=dataX, yVals=dataY, N=len(dataX))
else:
dataXlabel, dataYlabel = dataX, dataY
gifmap2 = HT.Map(name="CorrelationPlotImageMap2")
for i, item in enumerate(data_coordinate):
one_rect_coordinate = "%d, %d, %d, %d" % (item[0] - 6, item[1] - 6, item[0] + 6, item[1] + 6)
if isTissueCorr:
one_rect_title = "%s (%s, %s)" % (fullTissueName[i], dataXlabel[i], dataYlabel[i])
else:
one_rect_title = "%s (%s, %s)" % (dataZ[i], dataXlabel[i], dataYlabel[i])
gifmap2.areas.append(HT.Area(shape="rect", coords=one_rect_coordinate, title=one_rect_title))
filename = webqtlUtil.genRandStr("XY_")
c.save(webqtlConfig.IMGDIR + filename, format="gif")
img2 = HT.Image("/image/" + filename + ".gif", border=0, usemap="#CorrelationPlotImageMap2")
mainForm_2 = HT.Form(
cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
enctype="multipart/form-data",
name="showDatabase2",
submit=HT.Input(type="hidden"),
)
hddn = {
"FormID": "showDatabase2",
"ProbeSetID": "_",
"database": "_",
"CellID": "_",
"RISet": fd.RISet,
"ProbeSetID2": "_",
"database2": "_",
"CellID2": "_",
"allstrainlist": string.join(fd.strainlist, " "),
"traitList": fd.formdata.getvalue("traitList"),
}
if fd.incparentsf1:
hddn["incparentsf1"] = "ON"
for key in hddn.keys():
mainForm_2.append(HT.Input(name=key, value=hddn[key], type="hidden"))
if isSampleCorr:
mainForm_2.append(
HT.P(),
HT.Blockquote(
HT.Strong("X axis:"),
HT.Blockquote(trait2Url),
HT.Strong("Y axis:"),
HT.Blockquote(trait1Url),
style="width:%spx;" % self.plotSize,
),
)
TD_LR.append(HT.BR(), HT.P())
TD_LR.append("\n", gifmap2, HT.P(), HT.P(), img2, HT.P(), mainForm_2)
self.dict["body"] = str(TD_LR)
else:
heading = "Correlation Plot"
detail = [
"Fewer than %d strain data were entered for %s data set. No statitical analysis has been attempted."
% (self.corrMinInformative, fd.RISet)
]
self.error(heading=heading, detail=detail)
return
def insertCheckPage(self, fd, newRecord):
#generate html
form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), name='dataInput',submit=HT.Input(type='hidden'))
hddn = {'database':self.db.name, 'curStatus':'insertResult', 'FormID':'dataEditing', 'submitID':'addPublish', 'RISet':fd.RISet}
recordTable = HT.TableLite(border=0, align="left")
title1 = HT.Paragraph("Trait Information:", Class="subtitle")
title2 = HT.Paragraph("Trait Data:", Class="subtitle")
recordInfoContainer = HT.Div(align="left")
recordDataContainer = HT.Div(align="left")
addButton = HT.Input(type='submit',name='submit', value='Add to Publish',Class="button")
resetButton = HT.Input(type='reset',Class="button")
recordInfoTable = HT.TableLite(border=0, cellspacing=1, cellpadding=5, align="left")
for field in self.db.disfield:
if newRecord[field]:
recordInfoTable.append(HT.TR(
HT.TD("%s :" % webqtlUtil.formatField(field), Class="fs12 fwb ff1", valign="top",align="right"),
HT.TD(width=20),HT.TD(newRecord[field])))
hddn[field] = newRecord[field]
recordInfoContainer.append(addButton, resetButton, HT.P(), title1, HT.BR(), recordInfoTable)
recordDataTable = HT.TableLite(border=0, width = "80%",cellspacing=3, cellpadding=2)
recordDataTable.append(HT.TR(HT.TD('Strain Name',Class="fs12 ffl fwb",align="left"),
HT.TD('TraitData',Class="fs12 ffl fwb",align="right"),
HT.TD('SE',Class="fs12 ffl fwb",align="right"),
HT.TD('N Per Strain',Class="fs12 ffl fwb",align="right"),
HT.TD(' '*8,Class="fs12 ffl fwb",align="center"),
HT.TD('Strain Name',Class="fs12 ffl fwb",align="left"),
HT.TD('TraitData',Class="fs12 ffl fwb",align="right"),
HT.TD('SE',Class="fs12 ffl fwb",align="right"),
HT.TD('N Per Strain',Class="fs12 ffl fwb",align="right")))
tempTR = HT.TR(align="Center")
for i, strainName in enumerate(fd.strainlist):
if fd.allTraitData.has_key(strainName):
tdata = fd.allTraitData[strainName]
traitVal, traitVar, traitNP = tdata.val, tdata.var, tdata.N
else:
traitVal, traitVar, traitNP = None, None, None
if traitVal != None:
traitVal = "%2.3f" % traitVal
else:
traitVal = 'x'
if traitVar != None:
traitVar = "%2.3f" % traitVar
else:
traitVar = 'x'
if traitNP != None:
traitNP = "%d" % traitNP
else:
traitNP = 'x'
tempTR.append(HT.TD(HT.Paragraph(strainName),align='left'),
HT.TD(traitVal,align='right'),
HT.TD(traitVar,align='right'),
HT.TD(traitNP,align='right'),
HT.TD('',align='center'))
if i % 2:
recordDataTable.append(tempTR)
tempTR = HT.TR(align="Center")
if (i+1) % 2:
tempTR.append(HT.TD(''))
tempTR.append(HT.TD(''))
recordDataTable.append(tempTR)
info = HT.Paragraph("Please review the trait information and data in the text below. Check the values for errors. If no error is found, please click the \"Add to Publish\" button to submit it.")
recordDataContainer.append(title2, HT.BR(), info, HT.P(), recordDataTable, HT.P(), addButton, resetButton, HT.P())
recordTable.append(HT.TR(HT.TD(recordInfoContainer)), HT.TR(HT.TD(recordDataContainer)))
webqtlUtil.exportData(hddn, fd.allTraitData, 1)
for key in hddn.keys():
form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
#############################
TD_LR = HT.TD(valign="top",colspan=2,bgcolor="#ffffff")
mainTitle = HT.Paragraph("Add Trait to Published Database", Class="title")
form.append(recordTable)
TD_LR.append(mainTitle, HT.Blockquote(form))
self.dict['body'] = TD_LR
