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path: root/wqflask/basicStatistics/updatedBasicStatisticsPage.py
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-rwxr-xr-xwqflask/basicStatistics/updatedBasicStatisticsPage.py150
1 files changed, 150 insertions, 0 deletions
diff --git a/wqflask/basicStatistics/updatedBasicStatisticsPage.py b/wqflask/basicStatistics/updatedBasicStatisticsPage.py
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+++ b/wqflask/basicStatistics/updatedBasicStatisticsPage.py
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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-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