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 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 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()
class StatsTableDlg(QtGui.QDockWidget):
def __init__(self, preferences, parent=None, info=None):
QtGui.QDockWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_StatsTableDlg()
self.ui.setupUi(self)
self.preferences = preferences
self.table = ''
# signals
self.connect(self.ui.btnSave, QtCore.SIGNAL("clicked()"), self.saveTable)
self.connect(self.ui.chkShowActiveFeatures, QtCore.SIGNAL("clicked()"), self.__updateTable)
def updateTable(self, statsTest):
self.statsTest = statsTest
self.__updateTable()
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)
# resize columns to fit context by sampling first 100 rows
#self.ui.tableStatisticalSummary.resizeColumnsToContents()
for colIndex in xrange(0, self.table.columnCount(None)):
fm = self.ui.tableStatisticalSummary.fontMetrics()
maxWidth = fm.width(tableHeadings[colIndex]) + 10
for i in xrange(0, 100): # sample first 100 rows to estimate column width, this is strictly for efficiency
width = fm.width(self.ui.tableStatisticalSummary.model().data(self.ui.tableStatisticalSummary.model().index(i,colIndex), QtCore.Qt.DisplayRole).toString()) + 10
if width > maxWidth:
maxWidth = width
self.ui.tableStatisticalSummary.setColumnWidth(colIndex, maxWidth)
def saveTable(self):
filename = QtGui.QFileDialog.getSaveFileName(self, 'Save table...', self.preferences['Last directory'],
'Tab-separated values (*.tsv);;' +
'Text file (*.txt);;' +
'All files (*.*)')
if filename != '':
self.preferences['Last directory'] = filename[0:filename.lastIndexOf('/')]
try:
if self.table != '':
self.table.save(filename)
except IOError:
QtGui.QMessageBox.information(self, 'Failed to save table', 'Write permission for file denied.', QtGui.QMessageBox.Ok)
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()
class StatsTableDlg(QtGui.QDockWidget):
def __init__(self, preferences, parent=None, info=None):
QtGui.QDockWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_StatsTableDlg()
self.ui.setupUi(self)
self.preferences = preferences
self.table = ''
# signals
self.connect(self.ui.btnSave, QtCore.SIGNAL("clicked()"),
self.saveTable)
self.connect(self.ui.chkShowActiveFeatures, QtCore.SIGNAL("clicked()"),
self.__updateTable)
def updateTable(self, statsTest):
self.statsTest = statsTest
self.__updateTable()
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 saveTable(self):
filename = QtGui.QFileDialog.getSaveFileName(
self, 'Save table...', self.preferences['Last directory'],
'Tab-separated values (*.tsv);;' + 'Text file (*.txt);;' +
'All files (*.*)')
if filename != '':
self.preferences['Last directory'] = filename[0:filename.
lastIndexOf('/')]
try:
if self.table != '':
self.table.save(filename)
except IOError:
QtGui.QMessageBox.information(
self, 'Failed to save table',
'Write permission for file denied.', QtGui.QMessageBox.Ok)
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()
class StatsTableDlg(QtGui.QDockWidget):
def __init__(self, preferences, parent=None, info=None):
QtGui.QDockWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_StatsTableDlg()
self.ui.setupUi(self)
self.preferences = preferences
self.table = ''
# signals
self.connect(self.ui.btnSave, QtCore.SIGNAL("clicked()"), self.saveTable)
self.connect(self.ui.chkShowActiveFeatures, QtCore.SIGNAL("clicked()"), self.__updateTable)
def updateTable(self, statsTest):
self.statsTest = statsTest
self.__updateTable()
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 saveTable(self):
filename = QtGui.QFileDialog.getSaveFileName(self, 'Save table...', self.preferences['Last directory'],
'Tab-separated values (*.tsv);;' +
'Text file (*.txt);;' +
'All files (*.*)')
if filename != '':
self.preferences['Last directory'] = filename[0:filename.lastIndexOf('/')]
try:
if self.table != '':
self.table.save(filename)
except IOError:
QtGui.QMessageBox.information(self, 'Failed to save table', 'Write permission for file denied.', QtGui.QMessageBox.Ok)
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) # resize columns to fit context by sampling first 100 rows #self.ui.tableStatisticalSummary.resizeColumnsToContents() for colIndex in xrange(0, self.table.columnCount(None)): fm = self.ui.tableStatisticalSummary.fontMetrics() maxWidth = fm.width(tableHeadings[colIndex]) + 10 for i in xrange(0, 100): # sample first 100 rows to estimate column width, this is strictly for efficiency width = fm.width(self.ui.tableStatisticalSummary.model().data(self.ui.tableStatisticalSummary.model().index(i,colIndex), QtCore.Qt.DisplayRole).toString()) + 10 if width > maxWidth: maxWidth = width self.ui.tableStatisticalSummary.setColumnWidth(colIndex, maxWidth)
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()
class MainWindow(QtGui.QMainWindow):
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()
def appendCategoriesCOG(self):
assignCOGsDlg = AssignCOGsDlg(self)
assignCOGsDlg.exec_()
def profileTabClicked(self):
self.ui.widgetProfile.setVisible(not self.ui.widgetProfile.isVisible())
self.updateSideBarTabIcon(self.ui.widgetProfile,
self.ui.btnProfileArrow)
def statPropTabClicked(self):
self.ui.widgetStatisticalProp.setVisible(
not self.ui.widgetStatisticalProp.isVisible())
self.updateSideBarTabIcon(self.ui.widgetStatisticalProp,
self.ui.btnStatisticsArrow)
def filteringTabClicked(self):
self.ui.widgetFilter.setVisible(not self.ui.widgetFilter.isVisible())
self.updateSideBarTabIcon(self.ui.widgetFilter,
self.ui.btnFilteringArrow)
def updateSideBarTabIcon(self, tab, arrowButton):
icon = QtGui.QIcon()
if tab.isVisible():
icon.addPixmap(QtGui.QPixmap("icons/downArrow.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
else:
icon.addPixmap(QtGui.QPixmap("icons/rightArrow.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
arrowButton.setIcon(icon)
def prefrencesDlg(self):
preferencesDlg = PreferencesDlg(self)
preferencesDlg.ui.spinPseudoCount.setValue(
self.preferences['Pseudocount'])
preferencesDlg.ui.chkTruncateFeatureNames.setChecked(
self.preferences['Truncate feature names'])
preferencesDlg.ui.spinFeatureNameLength.setValue(
self.preferences['Length of truncated feature names'])
if preferencesDlg.exec_() == QtGui.QDialog.Accepted:
self.preferences[
'Pseudocount'] = preferencesDlg.ui.spinPseudoCount.value()
self.preferences[
'Truncate feature names'] = preferencesDlg.ui.chkTruncateFeatureNames.isChecked(
)
self.preferences[
'Length of truncated feature names'] = preferencesDlg.ui.spinFeatureNameLength.value(
)
self.exploratoryPlotUpdate()
self.statPlotUpdate()
def exploratoryPlotUpdate(self):
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
self.exploratoryPlots.update(self.profile)
QtGui.QApplication.instance().restoreOverrideCursor()
def exploratoryPlotConfigure(self):
if self.profile.getNumFeatures() != 0:
self.exploratoryPlots.configure(self.profile)
else:
QtGui.QMessageBox.information(
self, 'Invalid profile',
'A profile must be loaded before plots can be configured.',
QtGui.QMessageBox.Warning)
def statPlotUpdate(self):
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
self.statPlots.update(self.statsTest.results)
QtGui.QApplication.instance().restoreOverrideCursor()
def statPlotConfigure(self):
if self.statsTest.results.profile != None:
self.statPlots.configure(self.statsTest.results)
else:
QtGui.QMessageBox.information(
self, 'Invalid profile',
'Statistical test must be run before plots can be configured.',
QtGui.QMessageBox.Warning)
def sample1ColourDlg(self):
colour = QtGui.QColorDialog.getColor(
self.preferences['Sample 1 colour'], self, 'Colour for sample 1')
if colour.isValid():
self.preferences['Sample 1 colour'] = colour
self.setSample1Colour(colour)
def setSample1Colour(self, colour):
colourStr = str(colour.red()) + ',' + str(colour.green()) + ',' + str(
colour.blue())
self.ui.btnSample1Colour.setStyleSheet('* { background-color: rgb(' +
colourStr + ') }')
self.exploratoryPlotUpdate()
self.statPlotUpdate()
def sample2ColourDlg(self):
colour = QtGui.QColorDialog.getColor(
self.preferences['Sample 2 colour'], self, 'Colour for sample 2')
if colour.isValid():
self.preferences['Sample 2 colour'] = colour
self.setSample2Colour(colour)
def setSample2Colour(self, colour):
colourStr = str(colour.red()) + ',' + str(colour.green()) + ',' + str(
colour.blue())
self.ui.btnSample2Colour.setStyleSheet('* { background-color: rgb(' +
colourStr + ') }')
self.exploratoryPlotUpdate()
self.statPlotUpdate()
def createProfile(self):
createProfileDlg = CreateProfileDlg(self)
createProfileDlg.exec_()
def loadProfile(self):
# open file dialog
file = QtGui.QFileDialog.getOpenFileName(
self, 'Open profile', self.lastDirectory,
'STAMP profile file (*.spf *.txt);;All files (*.*)')
if file == '':
return
self.lastDirectory = file[0:file.lastIndexOf('/')]
# read profiles from file
try:
stampIO = StampIO(self.preferences)
self.profileTree, errMsg = stampIO.read(file)
if errMsg != None:
QtGui.QMessageBox.information(self, 'Error reading input file',
errMsg,
QtGui.QMessageBox.Warning)
return
except:
QtGui.QMessageBox.information(self, 'Error reading input file',
'Unknown parsing error.',
QtGui.QMessageBox.Warning)
return
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
# populate sample combo boxes
self.ui.cboSample1.clear()
self.ui.cboSample2.clear()
for name in self.profileTree.sampleNames:
self.ui.cboSample1.addItem(name)
self.ui.cboSample2.addItem(name)
self.ui.cboSample1.setCurrentIndex(
self.ui.cboSample1.findText(self.profileTree.sampleNames[0]))
self.ui.cboSample2.setCurrentIndex(
self.ui.cboSample2.findText(self.profileTree.sampleNames[1]))
# populate hierarchy combo boxes
self.ui.cboParentalLevel.clear()
self.ui.cboParentalLevel.addItem('Entire sample')
for header in self.profileTree.hierarchyHeadings[0:-1]:
self.ui.cboParentalLevel.addItem(header)
self.ui.cboParentalLevel.setCurrentIndex(0)
self.ui.cboProfileLevel.clear()
for header in self.profileTree.hierarchyHeadings:
self.ui.cboProfileLevel.addItem(header)
self.ui.cboProfileLevel.setCurrentIndex(0)
# indicate the hierarchical level of interest have changed
self.hierarchicalLevelsChanged()
QtGui.QApplication.instance().restoreOverrideCursor()
def parentLevelChanged(self):
parentDepth = self.profileTree.getHierarchicalLevelDepth(
str(self.ui.cboParentalLevel.currentText()))
profileDepth = self.profileTree.getHierarchicalLevelDepth(
str(self.ui.cboProfileLevel.currentText()))
if parentDepth >= profileDepth:
QtGui.QMessageBox.information(
self, 'Invalid profile',
'The parent level must be higher in the hierarchy than the profile level.',
QtGui.QMessageBox.Warning)
self.ui.cboParentalLevel.setCurrentIndex(0)
return
self.hierarchicalLevelsChanged()
def profileLevelChanged(self):
parentDepth = self.profileTree.getHierarchicalLevelDepth(
str(self.ui.cboParentalLevel.currentText()))
profileDepth = self.profileTree.getHierarchicalLevelDepth(
str(self.ui.cboProfileLevel.currentText()))
if profileDepth <= parentDepth:
QtGui.QMessageBox.information(
self, 'Invalid profile',
'The profile level must be deeper in the hierarchy than the parent level.',
QtGui.QMessageBox.Warning)
self.ui.cboProfileLevel.setCurrentIndex(
len(self.profileTree.hierarchyHeadings) - 1)
return
self.hierarchicalLevelsChanged()
def hierarchicalLevelsChanged(self):
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
# indicate that profile information has changed
refreshIcon = QtGui.QIcon()
refreshIcon.addPixmap(QtGui.QPixmap("icons/refresh.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.btnRunTest.setIcon(refreshIcon)
# create new profile
sampleName1 = str(self.ui.cboSample1.currentText())
sampleName2 = str(self.ui.cboSample2.currentText())
parentHeading = str(self.ui.cboParentalLevel.currentText())
profileHeading = str(self.ui.cboProfileLevel.currentText())
self.profile = self.profileTree.createProfile(sampleName1, sampleName2,
parentHeading,
profileHeading)
# update GUI to reflect new profile
self.ui.txtTotalSeqs1.setText(
str(self.profileTree.numSequencesInSample(sampleName1)))
self.ui.txtTotalSeqs2.setText(
str(self.profileTree.numSequencesInSample(sampleName2)))
self.ui.txtNumParentCategories.setText(
str(self.profile.getNumParentCategories()))
self.ui.txtNumFeatures.setText(str(self.profile.getNumFeatures()))
self.ui.cboHighlightHierarchyStats.setCurrentIndex(0)
self.ui.cboHighlightHierarchyExploratory.setCurrentIndex(0)
# populate highlight hierarchy combo box
profileIndex = self.profileTree.hierarchyHeadings.index(profileHeading)
self.ui.cboHighlightHierarchyStats.clear()
self.ui.cboHighlightHierarchyExploratory.clear()
self.ui.cboHighlightHierarchyStats.addItem('None')
self.ui.cboHighlightHierarchyExploratory.addItem('None')
for header in self.profileTree.hierarchyHeadings[0:profileIndex + 1]:
self.ui.cboHighlightHierarchyStats.addItem(header)
self.ui.cboHighlightHierarchyExploratory.addItem(header)
self.ui.cboHighlightHierarchyStats.setCurrentIndex(0)
self.ui.cboHighlightHierarchyExploratory.setCurrentIndex(0)
self.ui.cboHighlightFeatureStats.clear()
self.ui.cboHighlightFeatureExploratory.clear()
# indicate that any previously calculated results, plots, or tables are now invalid
self.exploratoryPlots.reset(self.preferences)
self.statPlots.reset(self.preferences)
selectedFeatures = self.statsTest.results.getSelectedFeatures()
self.statsTest = StatsTests()
self.statsTest.results.setSelectedFeatures(selectedFeatures)
self.statPlotUpdate()
self.updateFilterInfo()
self.populateSummaryTable()
self.exploratoryPlotUpdate()
QtGui.QApplication.instance().restoreOverrideCursor()
def runTest(self):
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
# indicate data is up-to-date
noIcon = QtGui.QIcon()
self.ui.btnRunTest.setIcon(noIcon)
# show progress of test
progress = QtGui.QProgressDialog("Running statistical test...",
QtCore.QString(), 0,
len(self.profile.getFeatures()), self)
progress.setWindowTitle('Progress')
progress.setWindowModality(QtCore.Qt.WindowModal)
# run significance test
test = self.statTestDict[str(self.ui.cboStatTests.currentText())]
testType = str(self.ui.cboSignTestType.currentText())
confIntervMethod = self.confIntervMethodDict[str(
self.ui.cboConfIntervMethods.currentText())]
coverage = float(self.ui.cboNominalCoverage.currentText())
self.statsTest.run(test, testType, confIntervMethod, coverage,
self.profile, progress)
# apply multiple test correction
multCompClass = self.multCompDict[str(
self.ui.cboMultCompMethod.currentText())]
self.statsTest.results.performMultCompCorrection(multCompClass)
# apply filters
self.applyFilters()
QtGui.QApplication.instance().restoreOverrideCursor()
def statTestPropChanged(self):
refreshIcon = QtGui.QIcon()
refreshIcon.addPixmap(QtGui.QPixmap("icons/refresh.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.btnRunTest.setIcon(refreshIcon)
def multCompCorrectionChanged(self):
multCompClass = self.multCompDict[str(
self.ui.cboMultCompMethod.currentText())]
if multCompClass.method == 'False discovery rate':
self.ui.lblSignLevelFilter.setText('q-value filter (>):')
else:
self.ui.lblSignLevelFilter.setText('p-value filter (>):')
self.statTestPropChanged()
def multCompCorrectionInfo(self):
if self.statsTest.results.multCompCorrection != None:
multCompDlg = MultCompCorrectionInfoDlg(
self,
self.statsTest.results.multCompCorrection.additionalInfo())
multCompDlg.exec_()
else:
QtGui.QMessageBox.information(self, 'Run test',
'Run hypothesis test first.',
QtGui.QMessageBox.Ok)
def seqFilterChanged(self):
if self.ui.cboSeqFilter.currentText() == 'maximum':
self.ui.lblSeqFilterSample1.setText('Maximum (<):')
elif self.ui.cboSeqFilter.currentText() == 'minimum':
self.ui.lblSeqFilterSample1.setText('Minimum (<):')
elif self.ui.cboSeqFilter.currentText() == 'independent':
self.ui.lblSeqFilterSample1.setText('Sample 1 (<):')
self.filteringPropChanged()
def parentSeqFilterChanged(self):
if self.ui.cboParentSeqFilter.currentText() == 'maximum':
self.ui.lblParentSeqFilterSample1.setText('Maximum (<):')
elif self.ui.cboParentSeqFilter.currentText() == 'minimum':
self.ui.lblParentSeqFilterSample1.setText('Minimum (<):')
elif self.ui.cboParentSeqFilter.currentText() == 'independent':
self.ui.lblParentSeqFilterSample1.setText('Sample 1 (<):')
self.filteringPropChanged()
def changeEffectSizeMeasure(self):
self.filteringPropChanged()
def filteringPropChanged(self):
# indicate that profile information has changed
refreshIcon = QtGui.QIcon()
refreshIcon.addPixmap(QtGui.QPixmap("icons/refresh.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.btnApplyFilters.setIcon(refreshIcon)
self.ui.btnSelectFeatures.setEnabled(
self.ui.chkSelectFeatures.isChecked())
self.ui.spinSignLevelFilter.setEnabled(
self.ui.chkEnableSignLevelFilter.isChecked())
self.ui.cboSeqFilter.setEnabled(self.ui.chkEnableSeqFilter.isChecked())
self.ui.spinFilterSample1.setEnabled(
self.ui.chkEnableSeqFilter.isChecked())
self.ui.spinFilterSample2.setEnabled(
self.ui.chkEnableSeqFilter.isChecked()
and self.ui.cboSeqFilter.currentText() == 'independent')
self.ui.lblSeqFilterSample2.setEnabled(
self.ui.cboSeqFilter.currentText() == 'independent')
self.ui.cboParentSeqFilter.setEnabled(
self.ui.chkEnableParentSeqFilter.isChecked())
self.ui.spinParentFilterSample1.setEnabled(
self.ui.chkEnableParentSeqFilter.isChecked())
self.ui.spinParentFilterSample2.setEnabled(
self.ui.chkEnableParentSeqFilter.isChecked()
and self.ui.cboParentSeqFilter.currentText() == 'independent')
self.ui.lblParentSeqFilterSample2.setEnabled(
self.ui.cboParentSeqFilter.currentText() == 'independent')
self.ui.cboEffectSizeMeasure1.setEnabled(
self.ui.chkEnableEffectSizeFilter1.isChecked())
self.ui.spinMinEffectSize1.setEnabled(
self.ui.chkEnableEffectSizeFilter1.isChecked())
self.ui.cboEffectSizeMeasure2.setEnabled(
self.ui.chkEnableEffectSizeFilter2.isChecked())
self.ui.spinMinEffectSize2.setEnabled(
self.ui.chkEnableEffectSizeFilter2.isChecked())
def selectFeaturesCheckbox(self):
self.filteringPropChanged()
def selectFeaturesDlg(self):
selectFeatureDialog = SelectFeaturesDlg(self.statsTest.results, self)
if selectFeatureDialog.exec_() == QtGui.QDialog.Accepted:
selectedFeatures = selectFeatureDialog.getSelectedFeatures()
self.statsTest.results.setSelectedFeatures(selectedFeatures)
self.filteringPropChanged()
def applyFilters(self):
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
icon = QtGui.QIcon()
self.ui.btnApplyFilters.setIcon(icon)
if not self.ui.chkSelectFeatures.isChecked():
self.statsTest.results.selectAllFeautres()
# perform filtering
signLevelFilter = self.ui.spinSignLevelFilter.value()
if not self.ui.chkEnableSignLevelFilter.isChecked():
signLevelFilter = None
# sequence filtering
seqFilter = str(self.ui.cboSeqFilter.currentText())
sample1Filter = int(self.ui.spinFilterSample1.value())
sample2Filter = int(self.ui.spinFilterSample2.value())
if not self.ui.chkEnableSeqFilter.isChecked():
seqFilter = None
sample1Filter = None
sample2Filter = None
parentSeqFilter = str(self.ui.cboParentSeqFilter.currentText())
parentSample1Filter = int(self.ui.spinParentFilterSample1.value())
parentSample2Filter = int(self.ui.spinParentFilterSample2.value())
if not self.ui.chkEnableParentSeqFilter.isChecked():
parentSeqFilter = None
parentSample1Filter = None
parentSample2Filter = None
# effect size filters
if self.ui.chkEnableEffectSizeFilter1.isChecked():
effectSizeMeasure1 = self.effectSizeDict[str(
self.ui.cboEffectSizeMeasure1.currentText())]
minEffectSize1 = float(self.ui.spinMinEffectSize1.value())
else:
effectSizeMeasure1 = None
minEffectSize1 = None
if self.ui.chkEnableEffectSizeFilter2.isChecked():
effectSizeMeasure2 = self.effectSizeDict[str(
self.ui.cboEffectSizeMeasure2.currentText())]
minEffectSize2 = float(self.ui.spinMinEffectSize2.value())
else:
effectSizeMeasure2 = None
minEffectSize2 = None
if self.ui.radioOR.isChecked():
effectSizeOperator = 'OR'
else:
effectSizeOperator = 'AND'
self.statsTest.results.filterFeatures(
signLevelFilter, seqFilter, sample1Filter, sample2Filter,
parentSeqFilter, parentSample1Filter, parentSample2Filter,
effectSizeMeasure1, minEffectSize1, effectSizeOperator,
effectSizeMeasure2, minEffectSize2)
self.updateFilterInfo()
# update table summarizing statistical results
self.populateSummaryTable()
# update plots
self.statPlots.update(self.statsTest.results)
QtGui.QApplication.instance().restoreOverrideCursor()
def updateFilterInfo(self):
self.ui.txtNumActiveFeatures.setText(
str(len(self.statsTest.results.getActiveFeatures())))
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 highlightHierarchyExploratoryChanged(self):
index = self.ui.cboHighlightHierarchyExploratory.currentIndex() - 1
if index == -1:
self.preferences['Selected exploratory features'] = []
self.ui.cboHighlightFeatureExploratory.clear()
self.exploratoryPlotUpdate()
return
features = set([])
for feature in self.profile.profileDict.keys():
hierarchy = self.profile.getHierarchy(feature)
features.add(hierarchy[index])
features = list(features)
features.sort(key=string.lower)
featureStrList = QtCore.QStringList()
for feature in features:
featureStrList.append(feature)
self.ui.cboHighlightFeatureExploratory.clear()
self.ui.cboHighlightFeatureExploratory.insertItems(
len(featureStrList), featureStrList)
self.ui.cboHighlightFeatureExploratory.setCurrentIndex(0)
self.ui.cboHighlightFeatureExploratory.adjustSize()
self.highlightFeatureExploratoryChanged()
def highlightFeatureExploratoryChanged(self):
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
index = self.ui.cboHighlightHierarchyExploratory.currentIndex() - 1
selectedFeature = self.ui.cboHighlightFeatureExploratory.currentText()
self.preferences['Selected exploratory features'] = []
for feature in self.profile.profileDict.keys():
hierarchy = self.profile.getHierarchy(feature)
if hierarchy[index] == selectedFeature:
self.preferences['Selected exploratory features'].append(
feature)
self.exploratoryPlotUpdate()
QtGui.QApplication.instance().restoreOverrideCursor()
def highlightHierarchyStatsChanged(self):
index = self.ui.cboHighlightHierarchyStats.currentIndex() - 1
if index == -1:
self.preferences['Selected statistical features'] = []
self.ui.cboHighlightFeatureStats.clear()
self.statPlots.update(self.statsTest.results)
return
features = set([])
for feature in self.statsTest.results.getActiveFeatures():
hierarchy = self.statsTest.results.profile.getHierarchy(feature)
features.add(hierarchy[index])
features = list(features)
features.sort(key=string.lower)
featureStrList = QtCore.QStringList()
for feature in features:
featureStrList.append(feature)
self.ui.cboHighlightFeatureStats.clear()
self.ui.cboHighlightFeatureStats.insertItems(len(featureStrList),
featureStrList)
self.ui.cboHighlightFeatureStats.setCurrentIndex(0)
self.ui.cboHighlightFeatureStats.adjustSize()
self.highlightFeatureStatsChanged()
def highlightFeatureStatsChanged(self):
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
index = self.ui.cboHighlightHierarchyStats.currentIndex() - 1
selectedFeature = self.ui.cboHighlightFeatureStats.currentText()
self.preferences['Selected statistical features'] = []
for feature in self.statsTest.results.getActiveFeatures():
hierarchy = self.statsTest.results.profile.getHierarchy(feature)
if hierarchy[index] == selectedFeature:
self.preferences['Selected statistical features'].append(
feature)
self.statPlots.update(self.statsTest.results)
QtGui.QApplication.instance().restoreOverrideCursor()
def saveImageDlg(self):
tabWidget = self.ui.tabWidget
if tabWidget.tabText(tabWidget.currentIndex()) == 'Exploratory plots':
plotToSave = self.exploratoryPlots
elif tabWidget.tabText(
tabWidget.currentIndex()) == 'Statistical plots':
plotToSave = self.statPlots
else:
QtGui.QMessageBox.information(
self, 'Select plot',
'A plot tab must be active to save a plot.',
QtGui.QMessageBox.Ok)
return
file = QtGui.QFileDialog.getSaveFileName(
self, 'Save plot...', self.lastDirectory,
'Portable Network Graphics (*.png);;' +
'Portable Document Format (*.pdf);;' + 'PostScript (*.ps);;' +
'Encapsulated PostScript (*.eps);;' +
'Scalable Vector Graphics (*.svg)')
if file != '':
self.lastDirectory = file[0:file.lastIndexOf('/')]
try:
if file[len(file) -
3:len(file)] == 'png' or file[len(file) -
3:len(file)] == 'PNG':
dpi, ok = QtGui.QInputDialog.getInteger(
self, 'Desired resolution',
'Enter desired resolution (DPI) of image:', 300)
if ok:
plotToSave.save(str(file), dpi)
else:
plotToSave.save(str(file))
except IOError:
QtGui.QMessageBox.information(
self, 'Failed to save image',
'Write permission for file denied.', QtGui.QMessageBox.Ok)
def sendPlotToWindow(self):
tabWidget = self.ui.tabWidget
if tabWidget.tabText(tabWidget.currentIndex()) == 'Exploratory plots':
newWindow = self.exploratoryPlots.sendToNewWindow(self.profile)
elif tabWidget.tabText(
tabWidget.currentIndex()) == 'Statistical plots':
newWindow = self.statPlots.sendToNewWindow(self.statsTest.results)
else:
QtGui.QMessageBox.information(
self, 'Send plot to window',
'A plot tab must be active before it can be sent to a new window.',
QtGui.QMessageBox.Ok)
return
self.plotWindows.append(newWindow)
def saveTableDlg(self):
tabWidget = self.ui.tabWidget
if tabWidget.tabText(
tabWidget.currentIndex()) == 'Statistical results table':
tableToSave = self.summaryTable
elif tabWidget.tabText(tabWidget.currentIndex()) == 'CI coverage':
tableToSave = self.coverageTable
elif tabWidget.tabText(tabWidget.currentIndex()) == 'Power test':
tableToSave = self.powerTable
else:
QtGui.QMessageBox.information(
self, 'Select table',
'A table tab must be active to save a table.',
QtGui.QMessageBox.Ok)
return
filename = QtGui.QFileDialog.getSaveFileName(
self, 'Save table...', self.lastDirectory,
'Tab-separated values (*.tsv);;' + 'Text file (*.txt);;' +
'All files (*.*)')
if filename != '':
self.lastDirectory = filename[0:filename.lastIndexOf('/')]
try:
tableToSave.save(filename)
except IOError:
QtGui.QMessageBox.information(
self, 'Failed to save table',
'Write permission for file denied.', QtGui.QMessageBox.Ok)
def confIntervCoverage(self):
if self.statsTest.results.profile == None:
return
confIntervMethod = self.confIntervMethodDict[str(
self.ui.cboConfIntervMethods.currentText())]
coverage = float(self.ui.cboCoverage.currentText()) / 100.0
trials = int(self.ui.spinConfIntervTrials.value())
bootstrapRep = int(self.ui.spinConfIntervReplicates.value())
data = self.statsTest.results.contingencyTable(
self.ui.chkConfInterActiveFeature.isChecked())
progress = QtGui.QProgressDialog("", QtCore.QString(), 0,
len(data) * trials, self)
progress.setWindowTitle('Estimating CI coverage')
progress.setWindowModality(QtCore.Qt.WindowModal)
confIntervCoverage = ConfIntervCoverage()
tableData = confIntervCoverage.run(confIntervMethod, coverage, data,
trials, bootstrapRep, progress)
self.populateConfIntervCoverageTable(tableData)
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 powerTest(self):
if self.statsTest.results.profile == None:
return
test = self.statTestDict[str(self.ui.cboStatTests.currentText())]
signLevel = float(self.ui.cboPowerSignLevel.currentText())
trials = int(self.ui.spinPowerTrials.value())
bootstrapRep = int(self.ui.spinPowerReplicates.value())
data = self.statsTest.results.contingencyTable(
self.ui.chkPowerActiveFeature.isChecked())
progress = QtGui.QProgressDialog("", QtCore.QString(), 0,
len(data) * trials, self)
progress.setWindowTitle('Estimating power')
progress.setWindowModality(QtCore.Qt.WindowModal)
power = Power()
tableData = power.run(test, signLevel, data, trials, bootstrapRep,
progress)
self.populatePowerTestTable(tableData)
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 openAboutDlg(self):
QtGui.QMessageBox.about(
self, 'About...',
'STAMP: STatistical Analysis of Metagenomic Profiles\n\n'
'%s\n'
'%s\n'
'%s\n\n'
'%s' %
('Donovan Parks and Robert Beiko', 'v1.08', 'March 13, 2011',
'Program icon by Caihua (http://commons.wikimedia.org/wiki/File:Fairytale_colors.png)'
))
