# **************************************************************************
# *
# * Authors: Carlos Oscar Sorzano (info@kinestat.com)
# *
# * Kinestat Pharma
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'info@kinestat.com'
# *
# **************************************************************************
import pyworkflow.protocol.params as params
from .protocol_pkpd import ProtPKPD
from pkpd.objects import PKPDVariable
from scipy import stats
import numpy as np
[docs]class ProtPKPDStatsExp1Subgroups2Mean(ProtPKPD):
""" Compare two means from two subgroups from the same experiment .\n
Protocol created by http://www.kinestatpharma.com\n """
_label = 'Exp1 SubGr2 Mean'
#--------------------------- DEFINE param functions --------------------------------------------
def _defineParams(self, form):
form.addSection('Input')
form.addParam('inputExperiment', params.PointerParam, label="Input experiment", important=True,
pointerClass='PKPDExperiment',
help='Select an experiment with samples')
form.addParam('labelToCompare', params.StringParam, label="Label to compare", default="",
help='Name of the label to compare between the two subroups')
form.addParam('expression1', params.StringParam, label="Subgroup 1", default="",
help='For example, $(weight)<100 and $(sex)=="male"')
form.addParam('expression2', params.StringParam, label="Subgroup 2", default="",
help='For example, $(weight)>=100 and $(sex)=="male"')
#--------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
self._insertFunctionStep('runCompare',self.inputExperiment.get().getObjId(), self.labelToCompare.get(),
self.expression1.get(), self.expression2.get())
#--------------------------- STEPS functions --------------------------------------------
[docs] def runCompare(self, objId, labelToAdd, expression1, expression2):
fh = open(self._getPath("report.txt"),'w')
self.experiment = self.readExperiment(self.inputExperiment.get().fnPKPD)
x1 = [float(x) for x in self.experiment.getSubGroupLabels(self.expression1.get(),self.labelToCompare.get())]
x2 = [float(x) for x in self.experiment.getSubGroupLabels(self.expression2.get(),self.labelToCompare.get())]
self.doublePrint(fh,"Values in SubGroup 1: %s"%str(x1))
self.doublePrint(fh,"Values in SubGroup 2: %s"%str(x2))
self.doublePrint(fh,"Testing H0: mu1=mu2")
self.doublePrint(fh," ")
try:
[t,pval] = stats.ttest_ind(np.asarray(x1,np.double),np.asarray(x2,np.double),True)
self.doublePrint(fh,"T-test two independent samples (same variance): t-statistic=%f p-value=%f"%(t,pval))
except:
pass
try:
[t,pval] = stats.ttest_ind(x1,x2, False)
self.doublePrint(fh,"T-test two independent samples (different variance, Welch's test): t-statistic=%f p-value=%f"%(t,pval))
except:
pass
try:
[u,pval] = stats.mannwhitneyu(x1, x2, True)
self.doublePrint(fh,"Mann-Whitney U test for two independent samples: u-statistic=%f p-value=%f"%(u,pval))
except:
pass
fh.close()
#--------------------------- INFO functions --------------------------------------------
def _summary(self):
import os
msg=["Comparison between Subgroup1 (%s) and Subgroup2 (%s)"%(self.expression1.get(),self.expression2.get())]
msg.append(' ')
self.addFileContentToMessage(msg,self._getPath("report.txt"))
return msg
def _validate(self):
msg=[]
self.experiment = self.readExperiment(self.inputExperiment.get().fnPKPD,False)
if not self.labelToCompare.get() in self.experiment.variables:
msg.append("Cannot find %s amongst the experiment variables"%self.labelToCompare.get())
else:
variable = self.experiment.variables[self.labelToCompare.get()]
if variable.role != PKPDVariable.ROLE_LABEL:
msg.append("Variable %s is not a label"%self.labelToCompare.get())
if variable.varType != PKPDVariable.TYPE_NUMERIC:
msg.append("Variable %s is not a number"%self.labelToCompare.get())
return msg
[docs] def filterVarForWizard(self, v):
""" Define the type of variables required (used in wizard). """
return v.isNumeric() and v.isLabel()