def populateConfIntervCoverageTable(self, tableData):
confIntervMethodStr = str(self.ui.cboConfIntervMethods.currentText())
coverageStr = str(self.ui.cboCoverage.currentText()) + '%'
self.ui.lblCoverageTableTitle.setText('Method = ' +
confIntervMethodStr +
'; Nominal coverage = ' +
coverageStr)
tableHeadings = [str(self.ui.cboProfileLevel.currentText())]
tableHeadings += [
str(self.ui.cboSample1.currentText()),
str(self.ui.cboSample2.currentText())
]
tableHeadings += ['Parent seq. 1', 'Parent seq. 2']
tableHeadings += ['Rel. freq. 1 (%)', 'Rel. freq. 2 (%)']
tableHeadings += ['Mean coverage', 'Std. dev. coverage']
tableHeadings += [
'Mean coverage (features <= 5 seq.)',
'Std. dev. (features <= 5 seq.)'
]
tableHeadings += [
'Mean coverage (features > 5 seq.)',
'Std. dev. (features > 5 seq.)'
]
self.coverageTable = GenericTable(tableData, tableHeadings, self)
self.coverageTable.sort(0, QtCore.Qt.AscendingOrder
) # start with features in alphabetical order
self.ui.tableConfInterCoverage.setModel(self.coverageTable)
self.ui.tableConfInterCoverage.verticalHeader().setVisible(False)
self.ui.tableConfInterCoverage.resizeColumnsToContents()
def populateSummaryTable(self):
tableData = self.statsTest.results.tableData(
self.ui.chkShowActiveFeatures.isChecked())
oneMinAlphaStr = str(self.statsTest.results.oneMinusAlpha() * 100)
tableHeadings = list(self.profile.hierarchyHeadings)
tableHeadings += [
str(self.ui.cboSample1.currentText()),
str(self.ui.cboSample2.currentText())
]
tableHeadings += ['Parent seq. 1', 'Parent seq. 2']
tableHeadings += ['Rel. freq. 1 (%)', 'Rel. freq. 2 (%)']
tableHeadings += ['p-values', 'p-values (corrected)']
tableHeadings += ['Effect size']
tableHeadings += [oneMinAlphaStr + '% lower CI']
tableHeadings += [oneMinAlphaStr + '% upper CI']
tableHeadings += [
'Power (alpha = ' + str(self.statsTest.results.alpha) + ')'
]
tableHeadings += [
'Equal sample size (alpha = ' + str(self.statsTest.results.alpha) +
'; power = ' + str(self.statsTest.results.oneMinusBeta()) + ')'
]
self.summaryTable = GenericTable(tableData, tableHeadings, self)
self.summaryTable.sort(0, QtCore.Qt.AscendingOrder
) # start with features in alphabetical order
self.ui.tableSummary.setModel(self.summaryTable)
self.ui.tableSummary.verticalHeader().setVisible(False)
self.ui.tableSummary.resizeColumnsToContents()
def populatePowerTestTable(self, tableData):
testStr = str(self.ui.cboStatTests.currentText())
signLevel = float(self.ui.cboPowerSignLevel.currentText())
self.ui.lblPowerTestTitle.setText('Test = ' + testStr +
'; Significance level = ' +
str(signLevel))
tableHeadings = [str(self.ui.cboProfileLevel.currentText())]
tableHeadings += [
str(self.ui.cboSample1.currentText()),
str(self.ui.cboSample2.currentText())
]
tableHeadings += ['Parent seq. 1', 'Parent seq. 2']
tableHeadings += ['Rel. freq. 1 (%)', 'Rel. freq. 2 (%)']
tableHeadings += ['Mean power', 'Std. dev. power']
tableHeadings += [
'Mean power (features <= 5 seq.)', 'Std. dev. (features <= 5 seq.)'
]
tableHeadings += [
'Mean power (features > 5 seq.)', 'Std. dev. (features > 5 seq.)'
]
self.powerTable = GenericTable(tableData, tableHeadings, self)
self.powerTable.sort(0, QtCore.Qt.AscendingOrder
) # start with features in alphabetical order
self.ui.tablePower.setModel(self.powerTable)
self.ui.tablePower.verticalHeader().setVisible(False)
self.ui.tablePower.resizeColumnsToContents()
def __updateTable(self):
if self.statsTest.results.profile != None:
tableData, tableHeadings = self.statsTest.results.tableData(
self.ui.chkShowActiveFeatures.isChecked())
self.table = GenericTable(tableData, tableHeadings, self)
self.table.sort(0, QtCore.Qt.AscendingOrder
) # start with features in alphabetical order
self.ui.tableStatisticalSummary.setModel(self.table)
self.ui.tableStatisticalSummary.verticalHeader().setVisible(False)
self.ui.tableStatisticalSummary.resizeColumnsToContents()
def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
self.preferences = preferences
# initialize GUI
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.lastDirectory = ''
# load plot plugins
self.exploratoryPlots = PlotsManager(self.ui.cboExploratoryPlots,
self.ui.plotExploratoryScrollArea,
'Profile scatter plot')
self.exploratoryPlots.loadPlots(self.preferences,
'plugins/exploratoryPlots/')
self.statPlots = PlotsManager(self.ui.cboStatPlots,
self.ui.plotStatScrollArea,
'Extended error bar')
self.statPlots.loadPlots(self.preferences, 'plugins/statPlots/')
# load statistical technique plugins
pluginManager = PluginManager(self.preferences)
self.effectSizeDict = pluginManager.loadPlugins(
'plugins/effectSizeFilters/')
pluginManager.populateComboBox(self.effectSizeDict,
self.ui.cboEffectSizeMeasure1,
'Difference between proportions')
pluginManager.populateComboBox(self.effectSizeDict,
self.ui.cboEffectSizeMeasure2,
'Ratio of proportions')
self.statTestDict = pluginManager.loadPlugins(
'plugins/statisticalTests/')
pluginManager.populateComboBox(self.statTestDict, self.ui.cboStatTests,
'Fisher\'s exact test')
self.multCompDict = pluginManager.loadPlugins(
'plugins/multipleComparisonCorrections/')
pluginManager.populateComboBox(self.multCompDict,
self.ui.cboMultCompMethod,
'No correction')
self.confIntervMethodDict = pluginManager.loadPlugins(
'plugins/confidenceIntervalMethods/')
pluginManager.populateComboBox(self.confIntervMethodDict,
self.ui.cboConfIntervMethods,
'DP: Newcombe-Wilson')
# initialize class variables
self.profileTree = ProfileTree()
self.profile = Profile()
self.statsTest = StatsTests()
self.plotWindows = []
# initialize tables
self.summaryTable = GenericTable([], [], self)
self.coverageTable = GenericTable([], [], self)
self.powerTable = GenericTable([], [], self)
# connect menu items signals to slots
self.connect(self.ui.mnuFileOpenProfile, QtCore.SIGNAL('triggered()'),
self.loadProfile)
self.connect(self.ui.mnuFileCreateProfile,
QtCore.SIGNAL('triggered()'), self.createProfile)
self.connect(self.ui.mnuFileAppendCategoryCOG,
QtCore.SIGNAL('triggered()'), self.appendCategoriesCOG)
self.connect(self.ui.mnuFileSavePlot, QtCore.SIGNAL('triggered()'),
self.saveImageDlg)
self.connect(self.ui.mnuFileSaveTable, QtCore.SIGNAL('triggered()'),
self.saveTableDlg)
self.connect(self.ui.mnuFileExit, QtCore.SIGNAL('triggered()'),
QtCore.SLOT('close()'))
self.connect(self.ui.mnuViewSendPlotToWindow,
QtCore.SIGNAL('triggered()'), self.sendPlotToWindow)
self.connect(self.ui.mnuSettingsPreferences,
QtCore.SIGNAL('triggered()'), self.prefrencesDlg)
self.connect(self.ui.mnuHelpAbout, QtCore.SIGNAL('triggered()'),
self.openAboutDlg)
# widget controls in sidebar
self.connect(self.ui.btnProfileTab, QtCore.SIGNAL('clicked()'),
self.profileTabClicked)
self.connect(self.ui.btnProfileArrow, QtCore.SIGNAL('clicked()'),
self.profileTabClicked)
self.connect(self.ui.btnStatisticsTab, QtCore.SIGNAL('clicked()'),
self.statPropTabClicked)
self.connect(self.ui.btnStatisticsArrow, QtCore.SIGNAL('clicked()'),
self.statPropTabClicked)
self.connect(self.ui.btnFilteringTab, QtCore.SIGNAL('clicked()'),
self.filteringTabClicked)
self.connect(self.ui.btnFilteringArrow, QtCore.SIGNAL('clicked()'),
self.filteringTabClicked)
# connect profile widget signals to slots
self.connect(self.ui.cboSample1, QtCore.SIGNAL('activated(QString)'),
self.hierarchicalLevelsChanged)
self.connect(self.ui.cboSample2, QtCore.SIGNAL('activated(QString)'),
self.hierarchicalLevelsChanged)
self.connect(self.ui.btnSample1Colour, QtCore.SIGNAL('clicked()'),
self.sample1ColourDlg)
self.connect(self.ui.btnSample2Colour, QtCore.SIGNAL('clicked()'),
self.sample2ColourDlg)
self.connect(self.ui.cboProfileLevel,
QtCore.SIGNAL('activated(QString)'),
self.profileLevelChanged)
self.connect(self.ui.cboParentalLevel,
QtCore.SIGNAL('activated(QString)'),
self.parentLevelChanged)
# connect statistical test widget signals to slots
self.connect(self.ui.cboStatTests, QtCore.SIGNAL('activated(QString)'),
self.statTestPropChanged)
self.connect(self.ui.cboSignTestType,
QtCore.SIGNAL('activated(QString)'),
self.statTestPropChanged)
self.connect(self.ui.cboConfIntervMethods,
QtCore.SIGNAL('activated(QString)'),
self.statTestPropChanged)
self.connect(self.ui.cboNominalCoverage,
QtCore.SIGNAL('activated(QString)'),
self.statTestPropChanged)
self.connect(self.ui.btnRunTest, QtCore.SIGNAL('clicked()'),
self.runTest)
self.connect(self.ui.cboMultCompMethod,
QtCore.SIGNAL('activated(QString)'),
self.multCompCorrectionChanged)
self.connect(self.ui.btnMultCompCorrectionInfo,
QtCore.SIGNAL('clicked()'), self.multCompCorrectionInfo)
# connect filtering test widget signals to slots
self.connect(self.ui.chkSelectFeatures, QtCore.SIGNAL('toggled(bool)'),
self.selectFeaturesCheckbox)
self.connect(self.ui.btnSelectFeatures, QtCore.SIGNAL('clicked()'),
self.selectFeaturesDlg)
self.connect(self.ui.chkEnableSignLevelFilter,
QtCore.SIGNAL('toggled(bool)'), self.filteringPropChanged)
self.connect(self.ui.spinSignLevelFilter,
QtCore.SIGNAL('valueChanged(QString)'),
self.filteringPropChanged)
self.connect(self.ui.cboSeqFilter, QtCore.SIGNAL('activated(QString)'),
self.seqFilterChanged)
self.connect(self.ui.chkEnableSeqFilter,
QtCore.SIGNAL('toggled(bool)'), self.filteringPropChanged)
self.connect(self.ui.spinFilterSample1,
QtCore.SIGNAL('valueChanged(QString)'),
self.filteringPropChanged)
self.connect(self.ui.spinFilterSample2,
QtCore.SIGNAL('valueChanged(QString)'),
self.filteringPropChanged)
self.connect(self.ui.cboParentSeqFilter,
QtCore.SIGNAL('activated(QString)'),
self.parentSeqFilterChanged)
self.connect(self.ui.chkEnableParentSeqFilter,
QtCore.SIGNAL('toggled(bool)'), self.filteringPropChanged)
self.connect(self.ui.spinParentFilterSample1,
QtCore.SIGNAL('valueChanged(QString)'),
self.filteringPropChanged)
self.connect(self.ui.spinParentFilterSample2,
QtCore.SIGNAL('valueChanged(QString)'),
self.filteringPropChanged)
self.connect(self.ui.radioOR, QtCore.SIGNAL('clicked()'),
self.filteringPropChanged)
self.connect(self.ui.radioAND, QtCore.SIGNAL('clicked()'),
self.filteringPropChanged)
self.connect(self.ui.cboEffectSizeMeasure1,
QtCore.SIGNAL('activated(QString)'),
self.changeEffectSizeMeasure)
self.connect(self.ui.cboEffectSizeMeasure2,
QtCore.SIGNAL('activated(QString)'),
self.changeEffectSizeMeasure)
self.connect(self.ui.spinMinEffectSize1,
QtCore.SIGNAL('valueChanged(QString)'),
self.filteringPropChanged)
self.connect(self.ui.spinMinEffectSize2,
QtCore.SIGNAL('valueChanged(QString)'),
self.filteringPropChanged)
self.connect(self.ui.chkEnableEffectSizeFilter1,
QtCore.SIGNAL('toggled(bool)'), self.filteringPropChanged)
self.connect(self.ui.chkEnableEffectSizeFilter2,
QtCore.SIGNAL('toggled(bool)'), self.filteringPropChanged)
self.connect(self.ui.btnApplyFilters, QtCore.SIGNAL('clicked()'),
self.applyFilters)
# connect exploratory plot page widget signals to slots
self.connect(self.ui.cboExploratoryPlots,
QtCore.SIGNAL('activated(QString)'),
self.exploratoryPlotUpdate)
self.connect(self.ui.btnExploratoryConfigurePlot,
QtCore.SIGNAL('clicked()'), self.exploratoryPlotConfigure)
# connect statistical plot page widget signals to slots
self.connect(self.ui.cboStatPlots, QtCore.SIGNAL('activated(QString)'),
self.statPlotUpdate)
self.connect(self.ui.btnStatConfigurePlot, QtCore.SIGNAL('clicked()'),
self.statPlotConfigure)
self.connect(self.ui.cboHighlightHierarchyExploratory,
QtCore.SIGNAL('activated(QString)'),
self.highlightHierarchyExploratoryChanged)
self.connect(self.ui.cboHighlightFeatureExploratory,
QtCore.SIGNAL('activated(QString)'),
self.highlightFeatureExploratoryChanged)
self.connect(self.ui.cboHighlightHierarchyStats,
QtCore.SIGNAL('activated(QString)'),
self.highlightHierarchyStatsChanged)
self.connect(self.ui.cboHighlightFeatureStats,
QtCore.SIGNAL('activated(QString)'),
self.highlightFeatureStatsChanged)
# connect paired profile page widget signals to slots
self.connect(self.ui.chkShowActiveFeatures,
QtCore.SIGNAL('toggled(bool)'), self.populateSummaryTable)
# connect CI coverage page widget signals to slots
self.connect(self.ui.btnConfIntervCoverage, QtCore.SIGNAL('clicked()'),
self.confIntervCoverage)
# connect CI coverage page widget signals to slots
self.connect(self.ui.btnPowerTest, QtCore.SIGNAL('clicked()'),
self.powerTest)
# initialize dynamic GUI elements
self.seqFilterChanged()
self.parentSeqFilterChanged()
self.setSample1Colour(self.preferences['Sample 1 colour'])
self.setSample2Colour(self.preferences['Sample 2 colour'])
# show window maximized
self.resize(1100, 700)
self.showMaximized()
