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from htmlgen import HTMLgen2 as HT
from base.templatePage import templatePage
from dbFunction import webqtlDatabaseFunction
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-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 = 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")
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)
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)
normalplot_div = HT.Div(id="statstabs-5")
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)
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
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