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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /wqflask/basicStatistics/updatedBasicStatisticsPage.py
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'wqflask/basicStatistics/updatedBasicStatisticsPage.py')
-rwxr-xr-xwqflask/basicStatistics/updatedBasicStatisticsPage.py150
1 files changed, 0 insertions, 150 deletions
diff --git a/wqflask/basicStatistics/updatedBasicStatisticsPage.py b/wqflask/basicStatistics/updatedBasicStatisticsPage.py
deleted file mode 100755
index 3f30619d..00000000
--- a/wqflask/basicStatistics/updatedBasicStatisticsPage.py
+++ /dev/null
@@ -1,150 +0,0 @@
-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