def createResultsPage(f, parametric, uniqueName):
samples, data = fileData(f)
pid, pathwayName = getPathwayByFilename(f)
print "pathway:", pathwayName
if parametric:
imgFilename = rootDir + pngDir + uniqueName + '_' + pid + "_p_summary.png"
else:
imgFilename = rootDir + pngDir + uniqueName + '_' + pid + "_np_summary.png"
imgSize = (12, 5)
pathwayName, entitySummary, pngFile = imgFG.createPlotFromData(
pathwayName, imgSize, imgFilename, parametric, samples, data)
#print "pathway:", pathwayName, entitySummary['sample']
print "pathway:", pathwayName
basePNG = os.path.basename(pngFile)
page = initializePage(t=pathwayName + " -- " + uniqueName,
h="",
sort_list="[[8,1]]")
page.img(src=pngDir + basePNG, alt="Summary Plot")
page.p("Result table")
putSummaryTable(p=page, b="1", data=entitySummary, id="result_table")
fname = basePNG[:-4] + ".html"
writePageToFile(page, rootDir + fname)
summary = summarizePathway(samples, data, entitySummary)
return fname, pathwayName, summary
def createSampleListPage(path_f, parametric, uniqueName, red_label,
grey_label):
samples, data = fileData(path_f)
pid, pathwayName = getPathwayByFilename(path_f)
print "pathway:", pathwayName
if parametric:
imgFilename = pngDir + uniqueName + '_' + pid + "_p_summary.png"
else:
imgFilename = pngDir + uniqueName + '_' + pid + "_np_summary.png"
#print "#image file ", imgFilename, "root", rootDir, "png", pngDir
imgSize = (12, 5)
pathwayName, entitySummary, pngFile = imgFG.createPlotFromData(
pathwayName, imgSize, imgFilename, parametric, samples, data,
red_label, grey_label, class1, class2)
basePNG = os.path.basename(pngFile)
page, summary_tsv = initializePage(t=pathwayName + " -- " + uniqueName,
h="",
sort_list="[[8,1]]")
#ipl plot at top of page
#summary_tsv.write('<img src="%s" alt="Summary Plot"\n' % pngDir+basePNG)
#summary_tsv.write('Result table\n')
page.img(src=pngBase + basePNG, alt="Summary Plot")
page.p("Result table")
putSummaryTable(p=page,
b="1",
data=entitySummary,
id="result_table",
tsv=summary_tsv)
fname = basePNG[:-4] + ".html"
print "createSampleListPage"
writePageToFile(page, rootDir + fname)
summary = summarizePathway(samples, data, entitySummary)
return fname, pathwayName, summary