from __future__ import print_function #import string from math import * #import piddle as pid #import os from pprint import pformat as pf from corestats import Stats import reaper from htmlgen import HTMLgen2 as HT #from utility import Plot from utility import webqtlUtil from base import webqtlConfig from dbFunction import webqtlDatabaseFunction def basicStatsTable(vals, trait_type=None, cellid=None, heritability=None): st = {} # This is the dictionary where we'll put everything for the template valsOnly = [] dataXZ = vals[:] for i in range(len(dataXZ)): valsOnly.append(dataXZ[i][1]) (st['traitmean'], st['traitmedian'], st['traitvar'], st['traitstdev'], st['traitsem'], st['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 = sorted(vals, webqtlUtil.cmpOrder) print("data for stats is:", pf(dataXZ)) for num, item in enumerate(dataXZ): print(" %i - %s" % (num, item)) print(" length:", len(dataXZ)) st['min'] = dataXZ[0][1] st['max'] = dataXZ[-1][1] numbers = [x[1] for x in dataXZ] stats = Stats(numbers) at75 = stats.percentile(75) at25 = stats.percentile(25) print("Interquartile:", at75 - at25) #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'): #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")) st['range_log2'] = dataXZ[-1][1]-dataXZ[0][1] st['range_fold'] = pow(2.0, (dataXZ[-1][1]-dataXZ[0][1])) st['interquartile'] = pow(2.0, (dataXZ[int((st['N']-1)*3.0/4.0)][1]-dataXZ[int((st['N']-1)/4.0)][1])) #XZ, 04/01/2009: don't try to get H2 value for probe. if not cellid: if heritability: # This field needs to still be put into the Jinja2 template st['heritability'] = 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"))) # Lei Yan # 2008/12/19 return st 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) 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) filename= webqtlUtil.genRandStr("nP_") c.save(webqtlConfig.IMGDIR+filename, format='gif') img=HT.Image('/image/'+filename+'.gif',border=0) return img def plotBoxPlot(vals): 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 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) plotLink = HT.Span("More about ", HT.Href(text="Box Plots", url="http://davidmlane.com/hyperstat/A37797.html", target="_blank", Class="fs13")) 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