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-rwxr-xr-xwqflask/base/webqtlCaseData.py26
-rwxr-xr-xwqflask/utility/Plot.py100
-rwxr-xr-xwqflask/wqflask/show_trait/DataEditingPage.py154
-rw-r--r--wqflask/wqflask/templates/trait_data_and_analysis.html2
4 files changed, 103 insertions, 179 deletions
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 7805df06..25665c55 100755
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -37,6 +37,7 @@ class webqtlCaseData(object):
self.variance = variance # Trait Variance
self.num_cases = num_cases # Number of individuals/cases
self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word)
+ self.outlier = None # Not set to True/False until later
def __repr__(self):
str = ""
@@ -49,6 +50,14 @@ class webqtlCaseData(object):
return str
@property
+ def class_outlier(self):
+ """Template helper"""
+ if self.outlier:
+ return "outlier"
+ else:
+ return ""
+
+ @property
def display_value(self):
if self.value:
return "%2.3f" % self.value
@@ -63,20 +72,3 @@ class webqtlCaseData(object):
return "x"
- #try:
- # traitVar = thisvar
- # dispVar = "%2.3f" % thisvar
- #except:
- # traitVar = ''
- # dispVar = 'x'
-
- #try:
- # traitVal = thisval
- # dispVal = "%2.3f" % thisval
- #except:
- # traitVal = ''
- # dispVal = 'x'
-
-
- #def this_val_full(self):
- # strain_name = \ No newline at end of file
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 086f3d57..51a57a6d 100755
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -25,6 +25,13 @@
# Last updated by GeneNetwork Core Team 2010/10/20
#import piddle as pid
+
+from __future__ import print_function
+
+from pprint import pformat as pf
+
+print("Lysol")
+
from math import *
import random
import sys, os
@@ -32,6 +39,9 @@ from numarray import linear_algebra as la
from numarray import ones, array, dot, swapaxes
import reaper
+sys.path.append("..")
+print(sys.path)
+from basicStatistics import corestats
import svg
import webqtlUtil
@@ -254,6 +264,7 @@ def gmedian(lst2):
return lst[(N-1)/2]
def gpercentile(lst2, np):
+ """Obsolete - use percentile in corestats instead"""
lst = lst2[:]
N = len(lst)
if N == 0 or np > 100 or np < 0:
@@ -270,61 +281,41 @@ def gpercentile(lst2, np):
else:
return lst[k-1] + d*(lst[k] - lst[k-1])
-def findOutliers(vals):
-
- valsOnly = []
- dataXZ = vals[:]
- for i in range(len(dataXZ)):
- valsOnly.append(dataXZ[i][1])
-
- data = [('', valsOnly[:])]
-
- for item in data:
- itemvalue = item[1]
- nValue = len(itemvalue)
- catValue = []
-
- for item2 in itemvalue:
- try:
- tstrain, tvalue = item2
- except:
- tvalue = item2
- if nValue <= 4:
- continue
- else:
- catValue.append(tvalue)
-
- if catValue != []:
- lowHinge = gpercentile(catValue, 25)
- upHinge = gpercentile(catValue, 75)
- Hstep = 1.5*(upHinge - lowHinge)
+def find_outliers(vals):
+ """Calculates the upper and lower bounds of a set of sample/case values
+
+
+ >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537])
+ (11.252500000000001, 0.5364999999999993)
+
+ >>> >>> find_outliers([9,12,15,17,31,50,7,5,6,8])
+ (32.0, -8.0)
+
+ If there are no vals, returns None for the upper and lower bounds,
+ which code that calls it will have to deal with.
+ >>> find_outliers([])
+ (None, None)
+
+ """
- outlier = []
- extreme = []
+ print("xerxes vals is:", pf(vals))
- upperBound = upHinge + Hstep
- lowerBound = lowHinge - Hstep
+ if vals:
+ #print("vals is:", pf(vals))
+ stats = corestats.Stats(vals)
+ low_hinge = stats.percentile(25)
+ up_hinge = stats.percentile(75)
+ hstep = 1.5 * (up_hinge - low_hinge)
- for item in catValue:
- if item >= upHinge + 2*Hstep:
- extreme.append(item)
- elif item >= upHinge + Hstep:
- outlier.append(item)
- else:
- pass
+ upper_bound = up_hinge + hstep
+ lower_bound = low_hinge - hstep
- for item in catValue:
- if item <= lowHinge - 2*Hstep:
- extreme.append(item)
- elif item <= lowHinge - Hstep:
- outlier.append(item)
- else:
- pass
- else:
- upperBound = 1000
- lowerBound = -1000
+ else:
+ upper_bound = None
+ lower_bound = None
- return upperBound, lowerBound
+ print(pf(locals()))
+ return upper_bound, lower_bound
def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabel="Value"):
@@ -1281,3 +1272,12 @@ def BWSpectrum(n=100):
out.append(pid.Color(x,x,x));
x += step
return out
+
+
+def _test():
+ import doctest
+ doctest.testmod()
+
+
+if __name__=="__main__":
+ _test()
diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py
index 43f05f14..bb6156c3 100755
--- a/wqflask/wqflask/show_trait/DataEditingPage.py
+++ b/wqflask/wqflask/show_trait/DataEditingPage.py
@@ -1,5 +1,7 @@
from __future__ import absolute_import, print_function, division
+print("Google")
+
import string
import os
import cPickle
@@ -1673,7 +1675,7 @@ class DataEditingPage(templatePage):
#showHideMenuOptions.append(HT.Bold("&nbsp;&nbsp;Options:"), "&nbsp;"*5, showHideNoValue, "&nbsp;"*5, showHideOutliers, "&nbsp;"*5, resetButton, "&nbsp;"*5, exportButton)
#traitTableOptions.append(showHideMenuOptions,HT.BR(),HT.BR())
- #traitTableOptions.append(HT.Span("&nbsp;&nbsp;Outliers highlighted in ", HT.Bold("&nbsp;yellow&nbsp;", style="background-color:yellow;"), " can be hidden using the ",
+ #traitTableOptions.append(HT.Span("&nbsp;&nbsp;Outliers highlighted in ", HT.Bold("&nbsp;red&nbsp;", style="background-color:red;"), " can be hidden using the ",
# HT.Strong(" Hide Outliers "), " button,",HT.BR(),"&nbsp;&nbsp;and samples with no value (x) can be hidden by clicking ",
# HT.Strong(" Hide No Value "), "."), HT.BR())
@@ -1703,7 +1705,7 @@ class DataEditingPage(templatePage):
primary_strainlist = fd.parlist + allstrainlist_neworder
- primary_strains = self.addTrait2Table(fd=fd,
+ primary_strains = self.create_strain_objects(fd=fd,
varianceDataPage=varianceDataPage,
strainlist=primary_strainlist,
mainForm=mainForm,
@@ -1712,6 +1714,7 @@ class DataEditingPage(templatePage):
attribute_ids=attribute_ids,
attribute_names=attribute_names,
strains='primary')
+
other_strains = []
for strain in thisTrait.data.keys():
@@ -1727,7 +1730,7 @@ class DataEditingPage(templatePage):
other_strains.sort() #Sort other strains
other_strains = par_f1_strains + other_strains
- other_strains = self.addTrait2Table(fd=fd,
+ other_strains = self.create_strain_objects(fd=fd,
varianceDataPage=varianceDataPage,
strainlist=other_strains,
mainForm=mainForm,
@@ -1736,6 +1739,7 @@ class DataEditingPage(templatePage):
attribute_names=attribute_names,
strains='other')
+
#TODO: Figure out why this if statement is written this way - Zach
if (other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0]))
or (fd.f1list and thisTrait.data.has_key(fd.f1list[1]))):
@@ -1747,7 +1751,7 @@ class DataEditingPage(templatePage):
self.other_strains = other_strains
- def addTrait2Table(self, fd, varianceDataPage, strainlist, mainForm, thisTrait,
+ def create_strain_objects(self, fd, varianceDataPage, strainlist, mainForm, thisTrait,
other_strainsExist=None, attribute_ids=None,
attribute_names=None, strains='primary'):
@@ -1759,23 +1763,26 @@ class DataEditingPage(templatePage):
#XZ, Aug 23, 2010: I commented the code related to the display of animal case
#strainInfo = thisTrait.has_key('strainInfo') and thisTrait.strainInfo
- print("in addTrait2Table")
- table_body = []
- vals = []
-
-
- #################### Only used to find upperBound and lowerBound
+ print("in create_strain_objects")
+ #table_body = []
+
+ ################### Only used to find upperBound and lowerBound
+ #vals = []
#for strainNameOrig in strainlist:
# strainName = strainNameOrig.replace("_2nd_", "")
# print("pen: %s - %s" % (strainNameOrig, strainName))
- # thisval = thisTrait.data[strainName].value
- # thisvar = thisTrait.data[strainName].variance
- # thisValFull = [strainName, thisval, thisvar]
- #
- # vals.append(thisValFull)
+ # try:
+ # thisval = thisTrait.data[strainName].value
+ # thisvar = thisTrait.data[strainName].variance
+ # thisValFull = [strainName, thisval, thisvar]
+ #
+ # vals.append(thisValFull)
+ # except KeyError:
+ # print("**x** Skipping:", strainName)
#
#upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers.
+
the_strains = []
for counter, strainNameOrig in enumerate(strainlist, 1):
@@ -1790,107 +1797,15 @@ class DataEditingPage(templatePage):
print("No strain %s, let's create it now" % strainName)
strain = webqtlCaseData.webqtlCaseData(strainName)
print("zyt - strainNameOrig:", strainNameOrig)
- #trId = strainNameOrig
- #selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)")
-
-
- #try:
- # thisval, thisvar, thisNP = thisTrait.data[strainName].value, thisTrait.data[strainName].var, thisTrait.data[strainName].N
- # if thisNP:
- # mainForm.append(HT.Input(name='N'+strainName, value=thisNP, type='hidden'))
- # else:
- # pass
- #except:
- # thisval = thisvar = 'x'
-
- #thisval = thisTrait.data[strainName].value
- #thisvar = thisTrait.data[strainName].variance
- #thisTrait.data[strainName].num_cases
-
- #strain['strain_name'] = strainName
- #strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl')
-
- #if varianceDataPage:
- #try:
- # traitVar = thisvar
- # dispVar = "%2.3f" % thisvar
- #except:
- # traitVar = ''
- # dispVar = 'x'
-
- #if thisval == 'x':
- # traitVar = '' #ZS: Used to be 0, but it doesn't seem like a good idea for values of 0 to *always* be at the bottom when you sort; it makes more sense to put "nothing"
- #
- # #className = 'fs13 b1 c222 '
- # #valueClassName = 'fs13 b1 c222 valueField '
- # #rowClassName = 'novalue '
- #else:
- # if (thisval >= upperBound) or (thisval <= lowerBound):
- # strain['outlier'] = "outlier" # We're going to use this as a class, so we want it to be a word
- # #className = 'fs13 b1 c222 outlier '
- # #valueClassName = 'fs13 b1 c222 valueField '
- # #rowClassName = 'outlier'
- # else:
- # strain['outlier'] = "not_outlier"
- # #className = 'fs13 b1 c222 '
- # #valueClassName = 'fs13 b1 c222 valueField '
- # #rowClassName = ' '
- #
- #if varianceDataPage:
- # varClassName = valueClassName + str(traitVar)
- #valueClassName += str(traitVal)
-
- #if strainNameOrig == strainName:
- # if other_strainsExist and strainNameOrig in (fd.parlist + fd.f1list):
- # ########################################################################################################################################################
- # # ZS: Append value and variance to the value and variance input fields' list of classes; this is so the javascript can update the value when the user
- # # changes it. The updated value is then used when the table is sorted (tablesorter.js). This needs to be done because the "value" attribute is immutable.
- # #########################################################################################################################################################
- #
- # #valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal,
- # # onChange= "javascript:this.form['_2nd_%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName)
- # if varianceDataPage:
- # pass
- # #seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar,
- # # onChange= "javascript:this.form['V_2nd_%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName)
- # else:
- # pass
- # #valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, Class=valueClassName)
- # if varianceDataPage:
- # pass
- # #seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, Class=varClassName)
- #else:
- # pass
- # #valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVal,
- # #onChange= "javascript:this.form['%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName)
- # if varianceDataPage:
- # pass
- # #seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar,
- # # onChange= "javascript:this.form['V%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName)
+
if strains == 'primary':
strain.this_id = "Primary_" + str(counter)
- #table_row = HT.TR(Id="Primary_"+str(i+1), Class=rowClassName)
else:
strain.this_id = "Other_" + str(counter)
- #table_row = HT.TR(Id="Other_"+str(i+1), Class=rowClassName)
-
- #strain['value'] = traitVal
- #
- #strain['se'] = dispVar
- #if varianceDataPage:
- #table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className))
- #table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className))
- #table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className))
- #table_row.append(HT.TD("&plusmn;", width=20, align='center', Class=className))
- #table_row.append(HT.TD(seField, width=80, align='right', Id="SE_"+str(i)+"_"+strains, Class=className))
- #pass
- #else:
- #table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className))
- #table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className))
- #table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className))
- #pass
- if thisTrait and thisTrait.db and thisTrait.db.type =='ProbeSet':
+
+ #### For extra attribute columns; currently only used by two human datasets - Zach
+ if thisTrait and thisTrait.db and thisTrait.db.type == 'ProbeSet':
if len(attribute_ids) > 0:
#ZS: Get StrainId value for the next query
@@ -1929,6 +1844,8 @@ class DataEditingPage(templatePage):
attr_counter += 1
the_strains.append(strain)
#table_body.append(table_row)
+
+ do_outliers(the_strains)
print("*the_strains are [%i]: %s" % (len(the_strains), pf(the_strains)))
return the_strains
@@ -1975,3 +1892,18 @@ class DataEditingPage(templatePage):
sortby = ("", "")
return sortby
+
+
+
+def do_outliers(strain_objects):
+ values = [strain.value for strain in strain_objects if strain.value != None]
+ upper_bound, lower_bound = Plot.find_outliers(values)
+
+ for strain in strain_objects:
+ if strain.value:
+ if upper_bound and strain.value > upper_bound:
+ strain.outlier = True
+ elif lower_bound and strain.value < lower_bound:
+ strain.outlier = True
+ else:
+ strain.outlier = False
diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html
index 94ba0aad..3644b436 100644
--- a/wqflask/wqflask/templates/trait_data_and_analysis.html
+++ b/wqflask/wqflask/templates/trait_data_and_analysis.html
@@ -3076,7 +3076,7 @@
</tr>
{% for strain in strain_type %}
- <tr class="{{ strain.outlier }} value_se" id="{{ strain.this_id }}">
+ <tr class="{{ strain.class_outlier }} value_se" id="{{ strain.this_id }}">
<td class="fs13 b1 c222" align="right" width="45">
{{ loop.index }}
<input type="checkbox" name="selectCheck" class="checkbox edit_strain_checkbox" value="{{ strain.name }}" checked="checked">