Merge branch 'flask' of http://github.com/zsloan/genenetwork

1 files changed, 150 insertions, 0 deletions

diff --git a/wqflask/basicStatistics/updatedBasicStatisticsPage.py b/wqflask/basicStatistics/updatedBasicStatisticsPage.py
new file mode 100755
index 00000000..3f30619d
--- /dev/null
+++ b/wqflask/basicStatistics/updatedBasicStatisticsPage.py
@@ -0,0 +1,150 @@
+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