def configure(self, profile, statsResults):
configDlg = ConfigureDialog(Ui_BoxPlotDialog)
configDlg.ui.cboFieldToPlot.setCurrentIndex(configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
configDlg.ui.spinFigWidth.setValue(self.figWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.chkShowAverage.setChecked(self.bShowAverages)
configDlg.ui.chkShowPvalue.setChecked(self.bShowPvalue)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.fieldToPlot = str(configDlg.ui.cboFieldToPlot.currentText())
self.figWidth = configDlg.ui.spinFigWidth.value()
self.figHeight = configDlg.ui.spinFigHeight.value()
self.bShowAverages = configDlg.ui.chkShowAverage.isChecked()
self.bShowPvalue = configDlg.ui.chkShowPvalue.isChecked()
self.settings.setValue('group: ' + self.name + '/column width', self.figWidth)
self.settings.setValue('group: ' + self.name + '/height', self.figHeight)
self.settings.setValue('group: ' + self.name + '/field to plot', self.fieldToPlot)
self.settings.setValue('group: ' + self.name + '/show averages', self.bShowAverages)
self.settings.setValue('group: ' + self.name + '/show p-value', self.bShowPvalue)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
configDlg = ConfigureDialog(Ui_ScatterPlotDialog)
configDlg.ui.spinNumBins.setEnabled(self.bShowHistograms)
configDlg.ui.spinHistogramSize.setEnabled(self.bShowHistograms)
configDlg.ui.spinFigWidth.setValue(self.figWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.cboSpreadMethod.setCurrentIndex(
configDlg.ui.cboSpreadMethod.findText(self.spreadMethod))
configDlg.ui.spinNumBins.setValue(self.numBins)
configDlg.ui.spinHistogramSize.setValue(self.histogramSize)
configDlg.ui.chkShowHistogram.setChecked(self.bShowHistograms)
configDlg.ui.spinMarkerSize.setValue(self.markerSize)
configDlg.ui.chkShowR2.setChecked(self.bShowR2)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = configDlg.ui.spinFigWidth.value()
self.figHeight = configDlg.ui.spinFigHeight.value()
self.spreadMethod = configDlg.ui.cboSpreadMethod.currentText()
self.numBins = configDlg.ui.spinNumBins.value()
self.histogramSize = configDlg.ui.spinHistogramSize.value()
self.bShowHistograms = configDlg.ui.chkShowHistogram.isChecked()
self.markerSize = configDlg.ui.spinMarkerSize.value()
self.bShowR2 = configDlg.ui.chkShowR2.isChecked()
self.settings.setValue('group: ' + self.name + '/width',
self.figWidth)
self.settings.setValue('group: ' + self.name + '/height',
self.figHeight)
self.settings.setValue('group: ' + self.name + '/spread method',
self.spreadMethod)
self.settings.setValue('group: ' + self.name + '/bin',
self.numBins)
self.settings.setValue('group: ' + self.name + '/bin size',
self.histogramSize)
self.settings.setValue('group: ' + self.name + '/show histograms',
self.bShowHistograms)
self.settings.setValue('group: ' + self.name + '/marker size',
self.markerSize)
self.settings.setValue('group: ' + self.name + '/show R2',
self.bShowR2)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
configDlg = ConfigureDialog(Ui_ScatterPlotDialog)
configDlg.ui.spinNumBins.setEnabled(self.bShowHistograms)
configDlg.ui.spinHistogramSize.setEnabled(self.bShowHistograms)
configDlg.ui.spinFigWidth.setValue(self.figWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.cboSpreadMethod.setCurrentIndex(configDlg.ui.cboSpreadMethod.findText(self.spreadMethod))
configDlg.ui.spinNumBins.setValue(self.numBins)
configDlg.ui.spinHistogramSize.setValue(self.histogramSize)
configDlg.ui.chkShowHistogram.setChecked(self.bShowHistograms)
configDlg.ui.spinMarkerSize.setValue(self.markerSize)
configDlg.ui.chkShowR2.setChecked(self.bShowR2)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = configDlg.ui.spinFigWidth.value()
self.figHeight = configDlg.ui.spinFigHeight.value()
self.spreadMethod = configDlg.ui.cboSpreadMethod.currentText()
self.numBins = configDlg.ui.spinNumBins.value()
self.histogramSize = configDlg.ui.spinHistogramSize.value()
self.bShowHistograms = configDlg.ui.chkShowHistogram.isChecked()
self.markerSize = configDlg.ui.spinMarkerSize.value()
self.bShowR2 = configDlg.ui.chkShowR2.isChecked()
self.settings.setValue('group: ' + self.name + '/width', self.figWidth)
self.settings.setValue('group: ' + self.name + '/height', self.figHeight)
self.settings.setValue('group: ' + self.name + '/spread method', self.spreadMethod)
self.settings.setValue('group: ' + self.name + '/bin', self.numBins)
self.settings.setValue('group: ' + self.name + '/bin size', self.histogramSize)
self.settings.setValue('group: ' + self.name + '/show histograms', self.bShowHistograms)
self.settings.setValue('group: ' + self.name + '/marker size', self.markerSize)
self.settings.setValue('group: ' + self.name + '/show R2', self.bShowR2)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
configDlg = ConfigureDialog(Ui_PcaPlotDialog)
configDlg.ui.spinFigWidth.setValue(self.figWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.chkFixedPixelsPerUnitDistance.setChecked(self.bFixedPixelsPerUnitDistance)
configDlg.ui.spinFigHeight.setDisabled(configDlg.ui.chkFixedPixelsPerUnitDistance.isChecked())
configDlg.ui.spinMarkerSize.setValue(self.markerSize)
configDlg.ui.chkRotateLabels.setChecked(self.bRotateLabels)
configDlg.ui.chkPC1vsPC3.setChecked(self.bShowPC1vsPC3)
configDlg.ui.chkPC3vsPC2.setChecked(self.bShowPC3vsPC2)
if self.legendPos == 2:
configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 3:
configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
elif self.legendPos == 4:
configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 9:
configDlg.ui.radioLegendPosUpperCentre.setChecked(True)
elif self.legendPos == 1:
configDlg.ui.radioLegendPosUpperRight.setChecked(True)
else:
configDlg.ui.radioLegendPosNone.setChecked(True)
configDlg.ui.chkUniqueShapes.setChecked(self.bUniqueShapes)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = configDlg.ui.spinFigWidth.value()
self.figHeight = configDlg.ui.spinFigHeight.value()
self.bFixedPixelsPerUnitDistance = configDlg.ui.chkFixedPixelsPerUnitDistance.isChecked()
self.markerSize = configDlg.ui.spinMarkerSize.value()
self.bRotateLabels = configDlg.ui.chkRotateLabels.isChecked()
self.bShowPC1vsPC3 = configDlg.ui.chkPC1vsPC3.isChecked()
self.bShowPC3vsPC2 = configDlg.ui.chkPC3vsPC2.isChecked()
# legend position
if configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
elif configDlg.ui.radioLegendPosUpperCentre.isChecked() == True:
self.legendPos = 9
elif configDlg.ui.radioLegendPosLowerRight.isChecked() == True:
self.legendPos = 4
elif configDlg.ui.radioLegendPosUpperRight.isChecked() == True:
self.legendPos = 1
else:
self.legendPos = -1
self.bUniqueShapes = configDlg.ui.chkUniqueShapes.isChecked()
self.settings.setValue('group: ' + self.name + '/width', self.figWidth)
self.settings.setValue('group: ' + self.name + '/height', self.figHeight)
self.settings.setValue('group: ' + self.name + '/fixed pixels per unit distance', self.bFixedPixelsPerUnitDistance)
self.settings.setValue('group: ' + self.name + '/marker size', self.markerSize)
self.settings.setValue('group: ' + self.name + '/rotate pc3 labels', self.bRotateLabels)
self.settings.setValue('group: ' + self.name + '/showPC1vsPC3', self.bShowPC1vsPC3)
self.settings.setValue('group: ' + self.name + '/showPC3vsPC2', self.bShowPC3vsPC2)
self.settings.setValue('group: ' + self.name + '/legend position', self.legendPos)
self.settings.setValue('group: ' + self.name + '/unique shapes', self.bUniqueShapes)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
self.statsResults = statsResults
self.configDlg = ConfigureDialog(Ui_ExtendedErrorBarDialog)
# set enabled state of controls
self.configDlg.ui.chkShowStdDev.setChecked(self.bShowBarPlot)
self.configDlg.ui.spinEndCapSize.setValue(self.bShowBarPlot)
self.configDlg.ui.spinMinimumX.setEnabled(self.bCustomLimits)
self.configDlg.ui.spinMaximumX.setEnabled(self.bCustomLimits)
# set current value of controls
self.configDlg.ui.cboSortingField.setCurrentIndex(
self.configDlg.ui.cboSortingField.findText(self.sortingField))
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigRowHeight.setValue(self.figHeightPerRow)
self.configDlg.ui.chkShowBarPlot.setChecked(self.bShowBarPlot)
self.configDlg.ui.chkPValueLabels.setChecked(self.bShowPValueLabels)
self.configDlg.ui.chkCorrectedPvalues.setChecked(
self.bShowCorrectedPvalues)
self.configDlg.ui.chkCustomLimits.setChecked(self.bCustomLimits)
self.configDlg.ui.spinMinimumX.setValue(self.minX)
self.configDlg.ui.spinMaximumX.setValue(self.maxX)
self.configDlg.ui.spinMarkerSize.setValue(self.markerSize)
self.configDlg.ui.chkShowStdDev.setChecked(self.bShowStdDev)
self.configDlg.ui.spinEndCapSize.setValue(self.endCapSize)
if self.legendPos == 2:
self.configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 3:
self.configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
elif self.legendPos == 4:
self.configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 8:
self.configDlg.ui.radioLegendPosLowerCentre.setChecked(True)
else:
self.configDlg.ui.radioLegendPosNone.setChecked(True)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
self.sortingField = str(
self.configDlg.ui.cboSortingField.currentText())
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeightPerRow = self.configDlg.ui.spinFigRowHeight.value()
self.bShowBarPlot = self.configDlg.ui.chkShowBarPlot.isChecked()
self.bShowPValueLabels = self.configDlg.ui.chkPValueLabels.isChecked(
)
self.bShowCorrectedPvalues = self.configDlg.ui.chkCorrectedPvalues.isChecked(
)
self.bCustomLimits = self.configDlg.ui.chkCustomLimits.isChecked()
self.minX = self.configDlg.ui.spinMinimumX.value()
self.maxX = self.configDlg.ui.spinMaximumX.value()
self.markerSize = self.configDlg.ui.spinMarkerSize.value()
self.bShowStdDev = self.configDlg.ui.chkShowStdDev.isChecked()
self.endCapSize = self.configDlg.ui.spinEndCapSize.value()
# legend position
if self.configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif self.configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
elif self.configDlg.ui.radioLegendPosLowerCentre.isChecked(
) == True:
self.legendPos = 8
elif self.configDlg.ui.radioLegendPosLowerRight.isChecked(
) == True:
self.legendPos = 4
else:
self.legendPos = -1
self.settings.setValue('group: ' + self.name + '/width',
self.figWidth)
self.settings.setValue('group: ' + self.name + '/row height',
self.figHeightPerRow)
self.settings.setValue('group: ' + self.name + '/field',
self.sortingField)
self.settings.setValue(
'group: ' + self.name + '/sequences subplot',
self.bShowBarPlot)
self.settings.setValue('group: ' + self.name + '/p-value labels',
self.bShowPValueLabels)
self.settings.setValue(
'group: ' + self.name + '/show corrected p-values',
self.bShowCorrectedPvalues)
self.settings.setValue(
'group: ' + self.name + '/use custom limits',
self.bCustomLimits)
self.settings.setValue('group: ' + self.name + '/minimum',
self.minX)
self.settings.setValue('group: ' + self.name + '/maximum',
self.maxX)
self.settings.setValue('group: ' + self.name + '/marker size',
self.markerSize)
self.settings.setValue('group: ' + self.name + '/show std. dev.',
self.bShowStdDev)
self.settings.setValue('group: ' + self.name + '/end cap size',
self.endCapSize)
self.settings.setValue('group: ' + self.name + '/legend position',
self.legendPos)
self.plot(profile, statsResults)
QtGui.QApplication.instance().restoreOverrideCursor()
def configure(self, profile, statsResults):
configDlg = ConfigureDialog(Ui_BarPlotDialog)
configDlg.ui.cboFieldToPlot.setCurrentIndex(configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
configDlg.ui.spinFigColWidth.setValue(self.figColWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.chkShowAverage.setChecked(self.bShowAverages)
# legend position
if self.legendPos == 0:
configDlg.ui.radioLegendPosBest.setDown(True)
elif self.legendPos == 1:
configDlg.ui.radioLegendPosUpperRight.setChecked(True)
elif self.legendPos == 7:
configDlg.ui.radioLegendPosCentreRight.setChecked(True)
elif self.legendPos == 4:
configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 2:
configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 6:
configDlg.ui.radioLegendPosCentreLeft.setChecked(True)
elif self.legendPos == 3:
configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
else:
configDlg.ui.radioLegendPosNone.setChecked(True)
configDlg.ui.chkShowPvalue.setChecked(self.bShowPvalue)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.fieldToPlot = str(configDlg.ui.cboFieldToPlot.currentText())
self.figColWidth = configDlg.ui.spinFigColWidth.value()
self.figHeight = configDlg.ui.spinFigHeight.value()
self.bShowAverages = configDlg.ui.chkShowAverage.isChecked()
# legend position
if configDlg.ui.radioLegendPosBest.isChecked() == True:
self.legendPos = 0
elif configDlg.ui.radioLegendPosUpperRight.isChecked() == True:
self.legendPos = 1
elif configDlg.ui.radioLegendPosCentreRight.isChecked() == True:
self.legendPos = 7
elif configDlg.ui.radioLegendPosLowerRight.isChecked() == True:
self.legendPos = 4
elif configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif configDlg.ui.radioLegendPosCentreLeft.isChecked() == True:
self.legendPos = 6
elif configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
else:
self.legendPos = -1
self.bShowPvalue = configDlg.ui.chkShowPvalue.isChecked()
self.settings.setValue('group: ' + self.name + '/column width', self.figColWidth)
self.settings.setValue('group: ' + self.name + '/height', self.figHeight)
self.settings.setValue('group: ' + self.name + '/field to plot', self.fieldToPlot)
self.settings.setValue('group: ' + self.name + '/show averages', self.bShowAverages)
self.settings.setValue('group: ' + self.name + '/legend position', self.legendPos)
self.settings.setValue('group: ' + self.name + '/show p-value', self.bShowPvalue)
self.plot(profile, statsResults)
class ExtendedErrorBar(AbstractGroupPlotPlugin):
'''
Extended error bar plot.
'''
def __init__(self, preferences, parent=None):
AbstractGroupPlotPlugin.__init__(self, preferences, parent)
self.name = 'Extended error bar'
self.type = 'Statistical'
self.bSupportsHighlight = True
self.bPlotFeaturesIndividually = False
self.settings = preferences['Settings']
self.figWidth = self.settings.value('group: ' + self.name + '/width',
7.0).toDouble()[0]
self.figHeightPerRow = self.settings.value(
'group: ' + self.name + '/row height', 0.2).toDouble()[0]
self.sortingField = self.settings.value(
'group: ' + self.name + '/field', 'p-values').toString()
self.bShowBarPlot = self.settings.value(
'group: ' + self.name + '/sequences subplot', True).toBool()
self.bShowPValueLabels = self.settings.value(
'group: ' + self.name + '/p-value labels', True).toBool()
self.bShowCorrectedPvalues = self.settings.value(
'group: ' + self.name + '/show corrected p-values', True).toBool()
self.bCustomLimits = self.settings.value(
'group: ' + self.name + '/use custom limits', False).toBool()
self.minX = self.settings.value('group: ' + self.name + '/minimum',
0.0).toDouble()[0]
self.maxX = self.settings.value('group: ' + self.name + '/maximum',
1.0).toDouble()[0]
self.markerSize = self.settings.value(
'group: ' + self.name + '/marker size', 30).toInt()[0]
self.bShowStdDev = self.settings.value(
'group: ' + self.name + '/show std. dev.', False).toBool()
self.endCapSize = self.settings.value(
'group: ' + self.name + '/end cap size', 0.0).toInt()[0]
self.legendPos = self.settings.value(
'group: ' + self.name + '/legend position', -1).toInt()[0]
def mirrorProperties(self, plotToCopy):
self.name = plotToCopy.name
self.figWidth = plotToCopy.figWidth
self.figHeightPerRow = plotToCopy.figHeightPerRow
self.sortingField = plotToCopy.sortingField
self.bShowBarPlot = plotToCopy.bShowBarPlot
self.bShowPValueLabels = plotToCopy.bShowPValueLabels
self.bShowCorrectedPvalues = plotToCopy.bShowCorrectedPvalues
self.bCustomLimits = plotToCopy.bCustomLimits
self.minX = plotToCopy.minX
self.maxX = plotToCopy.maxX
self.markerSize = plotToCopy.markerSize
self.bShowStdDev = plotToCopy.bShowStdDev
self.endCapSize = plotToCopy.endCapSize
self.percentageOrSeqCount = plotToCopy.percentageOrSeqCount
self.legendPos = plotToCopy.legendPos
def plot(self, profile, statsResults):
# *** Check if there is sufficient data to generate the plot
if len(statsResults.activeData) <= 0:
self.emptyAxis()
return
features = statsResults.getColumn('Features')
if len(features) > 200:
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.ArrowCursor))
reply = QtGui.QMessageBox.question(
self, 'Continue?',
'Profile contains ' + str(len(features)) + ' features. ' +
'It may take several seconds to generate this plot. We recommend filtering your profile first. '
+ 'Do you wish to continue?', QtGui.QMessageBox.Yes,
QtGui.QMessageBox.No)
QtGui.QApplication.instance().restoreOverrideCursor()
if reply == QtGui.QMessageBox.No:
self.emptyAxis()
return
# *** Colour of plot elements
axesColour = str(self.preferences['Axes colour'].name())
group1Colour = str(
self.preferences['Group colours'][profile.groupName1].name())
group2Colour = str(
self.preferences['Group colours'][profile.groupName2].name())
# *** Colour of plot elements
highlightColor = (0.9, 0.9, 0.9)
# *** Sort data
if self.sortingField == 'p-values':
statsResults.activeData = TableHelper.SortTable(statsResults.activeData,\
[statsResults.dataHeadings['pValues']], False)
elif self.sortingField == 'Effect sizes':
statsResults.activeData = TableHelper.SortTable(statsResults.activeData,\
[statsResults.dataHeadings['EffectSize']],
True, True, False)
elif self.sortingField == 'Feature labels':
statsResults.activeData = TableHelper.SortTableStrCol(statsResults.activeData,\
statsResults.dataHeadings['Features'], False)
features = statsResults.getColumn(
'Features') # get sorted feature labels
# *** Create lists for each quantity of interest
if statsResults.multCompCorrection.method == 'False discovery rate':
pValueTitle = 'q-value'
else:
pValueTitle = 'p-value'
if self.bShowCorrectedPvalues:
pValueLabels = statsResults.getColumnAsStr('pValuesCorrected')
pValueTitle += ' (corrected)'
else:
pValueLabels = statsResults.getColumnAsStr('pValues')
effectSizes = statsResults.getColumn('EffectSize')
lowerCIs = statsResults.getColumn('LowerCI')
upperCIs = statsResults.getColumn('UpperCI')
ciTitle = (
'%.3g' %
(statsResults.oneMinusAlpha() * 100)) + '% confidence intervals'
# *** Truncate feature labels
highlightedFeatures = list(
self.preferences['Highlighted group features'])
if self.preferences['Truncate feature names']:
length = self.preferences['Length of truncated feature names']
for i in xrange(0, len(features)):
if len(features[i]) > length + 3:
features[i] = features[i][0:length] + '...'
for i in xrange(0, len(highlightedFeatures)):
if len(highlightedFeatures[i]) > length + 3:
highlightedFeatures[
i] = highlightedFeatures[i][0:length] + '...'
# *** Check that there is at least one significant feature
if len(features) <= 0:
self.emptyAxis('No significant features')
return
# *** Adjust effect size for axis scale
dominateInSample2 = []
percentage1 = []
percentage2 = []
for i in xrange(0, len(effectSizes)):
if statsResults.bConfIntervRatio:
if effectSizes[i] < 1:
# mirror CI across y-axis
effectSizes[i] = 1.0 / effectSizes[i]
lowerCI = effectSizes[i] - (1.0 / upperCIs[i])
upperCI = (1.0 / lowerCIs[i]) - effectSizes[i]
lowerCIs[i] = lowerCI
upperCIs[i] = upperCI
dominateInSample2.append(i)
else:
lowerCIs[i] = effectSizes[i] - lowerCIs[i]
upperCIs[i] = upperCIs[i] - effectSizes[i]
else:
lowerCIs[i] = effectSizes[i] - lowerCIs[i]
upperCIs[i] = upperCIs[i] - effectSizes[i]
if effectSizes[i] < 0.0:
dominateInSample2.append(i)
# *** Set figure size
if self.legendPos == 3 or self.legendPos == 4 or self.legendPos == 8: # bottom legend
heightBottomLabels = 0.56 # inches
else:
heightBottomLabels = 0.4 # inches
heightTopLabels = 0.25
plotHeight = self.figHeightPerRow * len(features)
self.imageWidth = self.figWidth
self.imageHeight = plotHeight + heightBottomLabels + heightTopLabels
if self.imageWidth > 256 or self.imageHeight > 256:
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.ArrowCursor))
self.emptyAxis()
reply = QtGui.QMessageBox.question(
self, 'Excessively large plot',
'The resulting plot is too large to display.')
QtGui.QApplication.instance().restoreOverrideCursor()
return
self.fig.set_size_inches(self.imageWidth, self.imageHeight)
# *** Determine width of y-axis labels
yLabelBounds = self.yLabelExtents(features, 8)
# *** Size plots which comprise the extended errorbar plot
self.fig.clear()
spacingBetweenPlots = 0.25 # inches
widthNumSeqPlot = 1.25 # inches
if self.bShowBarPlot == False:
widthNumSeqPlot = 0.0
spacingBetweenPlots = 0.0
widthPvalueLabels = 0.75 # inches
if self.bShowPValueLabels == False:
widthPvalueLabels = 0.1
yPlotOffsetFigSpace = heightBottomLabels / self.imageHeight
heightPlotFigSpace = plotHeight / self.imageHeight
xPlotOffsetFigSpace = yLabelBounds.width + 0.1 / self.imageWidth
pValueLabelWidthFigSpace = widthPvalueLabels / self.imageWidth
widthPlotFigSpace = 1.0 - pValueLabelWidthFigSpace - xPlotOffsetFigSpace
widthErrorBarPlot = widthPlotFigSpace * self.imageWidth - widthNumSeqPlot - spacingBetweenPlots
axInitAxis = self.fig.add_axes([
xPlotOffsetFigSpace, yPlotOffsetFigSpace, widthPlotFigSpace,
heightPlotFigSpace
])
divider = make_axes_locatable(axInitAxis)
divider.get_vertical()[0] = Size.Fixed(
len(features) * self.figHeightPerRow)
if self.bShowBarPlot == True:
divider.get_horizontal()[0] = Size.Fixed(widthNumSeqPlot)
axErrorbar = divider.new_horizontal(widthErrorBarPlot,
pad=spacingBetweenPlots,
sharey=axInitAxis)
self.fig.add_axes(axErrorbar)
else:
divider.get_horizontal()[0] = Size.Fixed(widthErrorBarPlot)
axErrorbar = axInitAxis
# *** Plot of sequences for each subsystem
if self.bShowBarPlot == True:
axNumSeq = axInitAxis
meanRelFreqSeqs1 = statsResults.getColumn('MeanRelFreq1')
meanRelFreqSeqs2 = statsResults.getColumn('MeanRelFreq2')
if self.bShowStdDev:
stdDev1 = statsResults.getColumn('StdDevRelFreq1')
stdDev2 = statsResults.getColumn('StdDevRelFreq2')
endCapSize = self.endCapSize
else:
stdDev1 = [0] * len(meanRelFreqSeqs1)
stdDev2 = [0] * len(meanRelFreqSeqs2)
endCapSize = 0
axNumSeq.barh(np.arange(len(features)) + 0.0,
meanRelFreqSeqs1,
height=0.3,
xerr=stdDev1,
color=group1Colour,
ecolor='black',
capsize=endCapSize)
axNumSeq.barh(np.arange(len(features)) - 0.3,
meanRelFreqSeqs2,
height=0.3,
xerr=stdDev2,
color=group2Colour,
ecolor='black',
capsize=endCapSize)
for value in np.arange(-0.5, len(features) - 1, 2):
axNumSeq.axhspan(value,
value + 1,
facecolor=highlightColor,
edgecolor='none',
zorder=-1)
axNumSeq.set_xlabel('Mean proportion (%)')
maxPercentage = max(max(meanRelFreqSeqs1), max(meanRelFreqSeqs2))
axNumSeq.set_xticks([0, maxPercentage])
axNumSeq.set_xlim([0, maxPercentage * 1.05])
maxPercentageStr = '%.1f' % maxPercentage
axNumSeq.set_xticklabels(['0.0', maxPercentageStr])
axNumSeq.set_yticks(np.arange(len(features)))
axNumSeq.set_yticklabels(features)
axNumSeq.set_ylim([-1, len(features)])
for label in axNumSeq.get_yticklabels():
if label.get_text() in highlightedFeatures:
label.set_color('red')
for a in axNumSeq.yaxis.majorTicks:
a.tick1On = False
a.tick2On = False
for a in axNumSeq.xaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for line in axNumSeq.yaxis.get_ticklines():
line.set_color(axesColour)
for line in axNumSeq.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in axNumSeq.spines.iteritems():
if loc in ['left', 'right', 'top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
# *** Plot confidence intervals for each subsystem
lastAxes = axErrorbar
markerSize = math.sqrt(float(self.markerSize))
axErrorbar.errorbar(effectSizes,
np.arange(len(features)),
xerr=[lowerCIs, upperCIs],
fmt='o',
ms=markerSize,
mfc=group1Colour,
mec='black',
ecolor='black',
zorder=10)
effectSizesSample2 = [
effectSizes[value] for value in dominateInSample2
]
axErrorbar.plot(effectSizesSample2,
dominateInSample2,
ls='',
marker='o',
ms=markerSize,
mfc=group2Colour,
mec='black',
zorder=100)
if statsResults.bConfIntervRatio:
axErrorbar.vlines(1,
-1,
len(features),
linestyle='dashed',
color=axesColour)
else:
axErrorbar.vlines(0,
-1,
len(features),
linestyle='dashed',
color=axesColour)
for value in np.arange(-0.5, len(features) - 1, 2):
axErrorbar.axhspan(value,
value + 1,
facecolor=highlightColor,
edgecolor='none',
zorder=1)
axErrorbar.set_title(ciTitle)
axErrorbar.set_xlabel('Difference in mean proportions (%)')
if self.bCustomLimits:
axErrorbar.set_xlim([self.minX, self.maxX])
else:
self.minX, self.maxX = axErrorbar.get_xlim()
if self.bShowBarPlot == False:
axErrorbar.set_yticks(np.arange(len(features)))
axErrorbar.set_yticklabels(features)
axErrorbar.set_ylim([-1, len(features)])
for label in axErrorbar.get_yticklabels():
if label.get_text(
) in self.preferences['Highlighted group features']:
label.set_color('red')
else:
for label in axErrorbar.get_yticklabels():
label.set_visible(False)
for a in axErrorbar.yaxis.majorTicks:
a.set_visible(False)
for a in axErrorbar.xaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for a in axErrorbar.yaxis.majorTicks:
a.tick1On = False
a.tick2On = False
for line in axErrorbar.yaxis.get_ticklines():
line.set_visible(False)
for line in axErrorbar.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in axErrorbar.spines.iteritems():
if loc in ['left', 'right', 'top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
# *** Show p-values on right of last plot
if self.bShowPValueLabels == True:
axRight = lastAxes.twinx()
axRight.set_yticks(np.arange(len(pValueLabels)))
axRight.set_yticklabels(pValueLabels)
axRight.set_ylim([-1, len(pValueLabels)])
axRight.set_ylabel(pValueTitle)
for a in axRight.yaxis.majorTicks:
a.tick1On = False
a.tick2On = False
# *** Legend
if self.legendPos != -1:
legend1 = Rectangle((0, 0), 1, 1, fc=group1Colour)
legend2 = Rectangle((0, 0), 1, 1, fc=group2Colour)
legend = self.fig.legend([legend1, legend2],
(profile.groupName1, profile.groupName2),
loc=self.legendPos,
ncol=2)
legend.get_frame().set_linewidth(0)
self.updateGeometry()
self.draw()
def configure(self, profile, statsResults):
self.statsResults = statsResults
self.configDlg = ConfigureDialog(Ui_ExtendedErrorBarDialog)
# set enabled state of controls
self.configDlg.ui.chkShowStdDev.setChecked(self.bShowBarPlot)
self.configDlg.ui.spinEndCapSize.setValue(self.bShowBarPlot)
self.configDlg.ui.spinMinimumX.setEnabled(self.bCustomLimits)
self.configDlg.ui.spinMaximumX.setEnabled(self.bCustomLimits)
# set current value of controls
self.configDlg.ui.cboSortingField.setCurrentIndex(
self.configDlg.ui.cboSortingField.findText(self.sortingField))
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigRowHeight.setValue(self.figHeightPerRow)
self.configDlg.ui.chkShowBarPlot.setChecked(self.bShowBarPlot)
self.configDlg.ui.chkPValueLabels.setChecked(self.bShowPValueLabels)
self.configDlg.ui.chkCorrectedPvalues.setChecked(
self.bShowCorrectedPvalues)
self.configDlg.ui.chkCustomLimits.setChecked(self.bCustomLimits)
self.configDlg.ui.spinMinimumX.setValue(self.minX)
self.configDlg.ui.spinMaximumX.setValue(self.maxX)
self.configDlg.ui.spinMarkerSize.setValue(self.markerSize)
self.configDlg.ui.chkShowStdDev.setChecked(self.bShowStdDev)
self.configDlg.ui.spinEndCapSize.setValue(self.endCapSize)
if self.legendPos == 2:
self.configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 3:
self.configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
elif self.legendPos == 4:
self.configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 8:
self.configDlg.ui.radioLegendPosLowerCentre.setChecked(True)
else:
self.configDlg.ui.radioLegendPosNone.setChecked(True)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
self.sortingField = str(
self.configDlg.ui.cboSortingField.currentText())
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeightPerRow = self.configDlg.ui.spinFigRowHeight.value()
self.bShowBarPlot = self.configDlg.ui.chkShowBarPlot.isChecked()
self.bShowPValueLabels = self.configDlg.ui.chkPValueLabels.isChecked(
)
self.bShowCorrectedPvalues = self.configDlg.ui.chkCorrectedPvalues.isChecked(
)
self.bCustomLimits = self.configDlg.ui.chkCustomLimits.isChecked()
self.minX = self.configDlg.ui.spinMinimumX.value()
self.maxX = self.configDlg.ui.spinMaximumX.value()
self.markerSize = self.configDlg.ui.spinMarkerSize.value()
self.bShowStdDev = self.configDlg.ui.chkShowStdDev.isChecked()
self.endCapSize = self.configDlg.ui.spinEndCapSize.value()
# legend position
if self.configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif self.configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
elif self.configDlg.ui.radioLegendPosLowerCentre.isChecked(
) == True:
self.legendPos = 8
elif self.configDlg.ui.radioLegendPosLowerRight.isChecked(
) == True:
self.legendPos = 4
else:
self.legendPos = -1
self.settings.setValue('group: ' + self.name + '/width',
self.figWidth)
self.settings.setValue('group: ' + self.name + '/row height',
self.figHeightPerRow)
self.settings.setValue('group: ' + self.name + '/field',
self.sortingField)
self.settings.setValue(
'group: ' + self.name + '/sequences subplot',
self.bShowBarPlot)
self.settings.setValue('group: ' + self.name + '/p-value labels',
self.bShowPValueLabels)
self.settings.setValue(
'group: ' + self.name + '/show corrected p-values',
self.bShowCorrectedPvalues)
self.settings.setValue(
'group: ' + self.name + '/use custom limits',
self.bCustomLimits)
self.settings.setValue('group: ' + self.name + '/minimum',
self.minX)
self.settings.setValue('group: ' + self.name + '/maximum',
self.maxX)
self.settings.setValue('group: ' + self.name + '/marker size',
self.markerSize)
self.settings.setValue('group: ' + self.name + '/show std. dev.',
self.bShowStdDev)
self.settings.setValue('group: ' + self.name + '/end cap size',
self.endCapSize)
self.settings.setValue('group: ' + self.name + '/legend position',
self.legendPos)
self.plot(profile, statsResults)
QtGui.QApplication.instance().restoreOverrideCursor()
def configure(self, profile, statsResults):
self.statsResults = statsResults
self.configDlg = ConfigureDialog(Ui_ExtendedErrorBarDialog)
# set enabled state of controls
self.configDlg.ui.chkShowStdDev.setChecked(self.bShowBarPlot)
self.configDlg.ui.spinEndCapSize.setValue(self.bShowBarPlot)
self.configDlg.ui.spinMinimumX.setEnabled(self.bCustomLimits)
self.configDlg.ui.spinMaximumX.setEnabled(self.bCustomLimits)
# set current value of controls
self.configDlg.ui.cboSortingField.setCurrentIndex(self.configDlg.ui.cboSortingField.findText(self.sortingField))
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigRowHeight.setValue(self.figHeightPerRow)
self.configDlg.ui.chkShowBarPlot.setChecked(self.bShowBarPlot)
self.configDlg.ui.chkPValueLabels.setChecked(self.bShowPValueLabels)
self.configDlg.ui.chkCorrectedPvalues.setChecked(self.bShowCorrectedPvalues)
self.configDlg.ui.chkCustomLimits.setChecked(self.bCustomLimits)
self.configDlg.ui.spinMinimumX.setValue(self.minX)
self.configDlg.ui.spinMaximumX.setValue(self.maxX)
self.configDlg.ui.spinMarkerSize.setValue(self.markerSize)
self.configDlg.ui.chkShowStdDev.setChecked(self.bShowStdDev)
self.configDlg.ui.spinEndCapSize.setValue(self.endCapSize)
if self.legendPos == 2:
self.configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 3:
self.configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
elif self.legendPos == 4:
self.configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 8:
self.configDlg.ui.radioLegendPosLowerCentre.setChecked(True)
else:
self.configDlg.ui.radioLegendPosNone.setChecked(True)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
QtGui.QApplication.instance().setOverrideCursor(QtGui.QCursor(QtCore.Qt.WaitCursor))
self.sortingField = str(self.configDlg.ui.cboSortingField.currentText())
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeightPerRow = self.configDlg.ui.spinFigRowHeight.value()
self.bShowBarPlot = self.configDlg.ui.chkShowBarPlot.isChecked()
self.bShowPValueLabels = self.configDlg.ui.chkPValueLabels.isChecked()
self.bShowCorrectedPvalues = self.configDlg.ui.chkCorrectedPvalues.isChecked()
self.bCustomLimits = self.configDlg.ui.chkCustomLimits.isChecked()
self.minX = self.configDlg.ui.spinMinimumX.value()
self.maxX = self.configDlg.ui.spinMaximumX.value()
self.markerSize = self.configDlg.ui.spinMarkerSize.value()
self.bShowStdDev = self.configDlg.ui.chkShowStdDev.isChecked()
self.endCapSize = self.configDlg.ui.spinEndCapSize.value()
# legend position
if self.configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif self.configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
elif self.configDlg.ui.radioLegendPosLowerCentre.isChecked() == True:
self.legendPos = 8
elif self.configDlg.ui.radioLegendPosLowerRight.isChecked() == True:
self.legendPos = 4
else:
self.legendPos = -1
self.settings.setValue('group: ' + self.name + '/width', self.figWidth)
self.settings.setValue('group: ' + self.name + '/row height', self.figHeightPerRow)
self.settings.setValue('group: ' + self.name + '/field', self.sortingField)
self.settings.setValue('group: ' + self.name + '/sequences subplot', self.bShowBarPlot)
self.settings.setValue('group: ' + self.name + '/p-value labels', self.bShowPValueLabels)
self.settings.setValue('group: ' + self.name + '/show corrected p-values', self.bShowCorrectedPvalues)
self.settings.setValue('group: ' + self.name + '/use custom limits', self.bCustomLimits)
self.settings.setValue('group: ' + self.name + '/minimum', self.minX)
self.settings.setValue('group: ' + self.name + '/maximum', self.maxX)
self.settings.setValue('group: ' + self.name + '/marker size', self.markerSize)
self.settings.setValue('group: ' + self.name + '/show std. dev.', self.bShowStdDev)
self.settings.setValue('group: ' + self.name + '/end cap size', self.endCapSize)
self.settings.setValue('group: ' + self.name + '/legend position', self.legendPos)
self.plot(profile, statsResults)
QtGui.QApplication.instance().restoreOverrideCursor()
class ExtendedErrorBar(AbstractGroupPlotPlugin):
'''
Extended error bar plot.
'''
def __init__(self, preferences, parent=None):
AbstractGroupPlotPlugin.__init__(self, preferences, parent)
self.name = 'Extended error bar'
self.type = 'Statistical'
self.bSupportsHighlight = True
self.bPlotFeaturesIndividually = False
self.settings = preferences['Settings']
self.figWidth = self.settings.value('group: ' + self.name + '/width', 7.0).toDouble()[0]
self.figHeightPerRow = self.settings.value('group: ' + self.name + '/row height', 0.2).toDouble()[0]
self.sortingField = self.settings.value('group: ' + self.name + '/field', 'p-values').toString()
self.bShowBarPlot = self.settings.value('group: ' + self.name + '/sequences subplot', True).toBool()
self.bShowPValueLabels = self.settings.value('group: ' + self.name + '/p-value labels', True).toBool()
self.bShowCorrectedPvalues = self.settings.value('group: ' + self.name + '/show corrected p-values', True).toBool()
self.bCustomLimits = self.settings.value('group: ' + self.name + '/use custom limits', False).toBool()
self.minX = self.settings.value('group: ' + self.name + '/minimum', 0.0).toDouble()[0]
self.maxX = self.settings.value('group: ' + self.name + '/maximum', 1.0).toDouble()[0]
self.markerSize = self.settings.value('group: ' + self.name + '/marker size', 30).toInt()[0]
self.bShowStdDev = self.settings.value('group: ' + self.name + '/show std. dev.', False).toBool()
self.endCapSize = self.settings.value('group: ' + self.name + '/end cap size', 0.0).toInt()[0]
self.legendPos = self.settings.value('group: ' + self.name + '/legend position', -1).toInt()[0]
def mirrorProperties(self, plotToCopy):
self.name = plotToCopy.name
self.figWidth = plotToCopy.figWidth
self.figHeightPerRow = plotToCopy.figHeightPerRow
self.sortingField = plotToCopy.sortingField
self.bShowBarPlot = plotToCopy.bShowBarPlot
self.bShowPValueLabels = plotToCopy.bShowPValueLabels
self.bShowCorrectedPvalues = plotToCopy.bShowCorrectedPvalues
self.bCustomLimits = plotToCopy.bCustomLimits
self.minX = plotToCopy.minX
self.maxX = plotToCopy.maxX
self.markerSize = plotToCopy.markerSize
self.bShowStdDev = plotToCopy.bShowStdDev
self.endCapSize = plotToCopy.endCapSize
self.percentageOrSeqCount = plotToCopy.percentageOrSeqCount
self.legendPos = plotToCopy.legendPos
def plot(self, profile, statsResults):
# *** Check if there is sufficient data to generate the plot
if len(statsResults.activeData) <= 0:
self.emptyAxis()
return
features = statsResults.getColumn('Features')
if len(features) > 200:
QtGui.QApplication.instance().setOverrideCursor(QtGui.QCursor(QtCore.Qt.ArrowCursor))
reply = QtGui.QMessageBox.question(self, 'Continue?', 'Profile contains ' + str(len(features)) + ' features. ' +
'It may take several seconds to generate this plot. We recommend filtering your profile first. ' +
'Do you wish to continue?', QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
QtGui.QApplication.instance().restoreOverrideCursor()
if reply == QtGui.QMessageBox.No:
self.emptyAxis()
return
# *** Colour of plot elements
axesColour = str(self.preferences['Axes colour'].name())
group1Colour = str(self.preferences['Group colours'][profile.groupName1].name())
group2Colour = str(self.preferences['Group colours'][profile.groupName2].name())
# *** Colour of plot elements
highlightColor = (0.9, 0.9, 0.9)
# *** Sort data
if self.sortingField == 'p-values':
statsResults.activeData = TableHelper.SortTable(statsResults.activeData,\
[statsResults.dataHeadings['pValues']], False)
elif self.sortingField == 'Effect sizes':
statsResults.activeData = TableHelper.SortTable(statsResults.activeData,\
[statsResults.dataHeadings['EffectSize']],
True, True, False)
elif self.sortingField == 'Feature labels':
statsResults.activeData = TableHelper.SortTableStrCol(statsResults.activeData,\
statsResults.dataHeadings['Features'], False)
features = statsResults.getColumn('Features') # get sorted feature labels
# *** Create lists for each quantity of interest
if statsResults.multCompCorrection.method == 'False discovery rate':
pValueTitle = 'q-value'
else:
pValueTitle = 'p-value'
if self.bShowCorrectedPvalues:
pValueLabels = statsResults.getColumnAsStr('pValuesCorrected')
pValueTitle += ' (corrected)'
else:
pValueLabels = statsResults.getColumnAsStr('pValues')
effectSizes = statsResults.getColumn('EffectSize')
lowerCIs = statsResults.getColumn('LowerCI')
upperCIs = statsResults.getColumn('UpperCI')
ciTitle = ('%.3g' % (statsResults.oneMinusAlpha()*100)) + '% confidence intervals'
# *** Truncate feature labels
highlightedFeatures = list(self.preferences['Highlighted group features'])
if self.preferences['Truncate feature names']:
length = self.preferences['Length of truncated feature names']
for i in xrange(0, len(features)):
if len(features[i]) > length+3:
features[i] = features[i][0:length] + '...'
for i in xrange(0, len(highlightedFeatures)):
if len(highlightedFeatures[i]) > length+3:
highlightedFeatures[i] = highlightedFeatures[i][0:length] + '...'
# *** Check that there is at least one significant feature
if len(features) <= 0:
self.emptyAxis('No significant features')
return
# *** Adjust effect size for axis scale
dominateInSample2 = []
percentage1 = []
percentage2 = []
for i in xrange(0, len(effectSizes)):
if statsResults.bConfIntervRatio:
if effectSizes[i] < 1:
# mirror CI across y-axis
effectSizes[i] = 1.0 / effectSizes[i]
lowerCI = effectSizes[i] - (1.0 / upperCIs[i])
upperCI = (1.0 / lowerCIs[i]) - effectSizes[i]
lowerCIs[i] = lowerCI
upperCIs[i] = upperCI
dominateInSample2.append(i)
else:
lowerCIs[i] = effectSizes[i] - lowerCIs[i]
upperCIs[i] = upperCIs[i] - effectSizes[i]
else:
lowerCIs[i] = effectSizes[i] - lowerCIs[i]
upperCIs[i] = upperCIs[i] - effectSizes[i]
if effectSizes[i] < 0.0:
dominateInSample2.append(i)
# *** Set figure size
if self.legendPos == 3 or self.legendPos == 4 or self.legendPos == 8: # bottom legend
heightBottomLabels = 0.56 # inches
else:
heightBottomLabels = 0.4 # inches
heightTopLabels = 0.25
plotHeight = self.figHeightPerRow*len(features)
self.imageWidth = self.figWidth
self.imageHeight = plotHeight + heightBottomLabels + heightTopLabels
if self.imageWidth > 256 or self.imageHeight > 256:
QtGui.QApplication.instance().setOverrideCursor(QtGui.QCursor(QtCore.Qt.ArrowCursor))
self.emptyAxis()
reply = QtGui.QMessageBox.question(self, 'Excessively large plot', 'The resulting plot is too large to display.')
QtGui.QApplication.instance().restoreOverrideCursor()
return
self.fig.set_size_inches(self.imageWidth, self.imageHeight)
# *** Determine width of y-axis labels
yLabelBounds = self.yLabelExtents(features, 8)
# *** Size plots which comprise the extended errorbar plot
self.fig.clear()
spacingBetweenPlots = 0.25 # inches
widthNumSeqPlot = 1.25 # inches
if self.bShowBarPlot == False:
widthNumSeqPlot = 0.0
spacingBetweenPlots = 0.0
widthPvalueLabels = 0.75 # inches
if self.bShowPValueLabels == False:
widthPvalueLabels = 0.1
yPlotOffsetFigSpace = heightBottomLabels / self.imageHeight
heightPlotFigSpace = plotHeight / self.imageHeight
xPlotOffsetFigSpace = yLabelBounds.width + 0.1 / self.imageWidth
pValueLabelWidthFigSpace = widthPvalueLabels / self.imageWidth
widthPlotFigSpace = 1.0 - pValueLabelWidthFigSpace - xPlotOffsetFigSpace
widthErrorBarPlot = widthPlotFigSpace*self.imageWidth - widthNumSeqPlot - spacingBetweenPlots
axInitAxis = self.fig.add_axes([xPlotOffsetFigSpace,yPlotOffsetFigSpace,widthPlotFigSpace,heightPlotFigSpace])
divider = make_axes_locatable(axInitAxis)
divider.get_vertical()[0] = Size.Fixed(len(features)*self.figHeightPerRow)
if self.bShowBarPlot == True:
divider.get_horizontal()[0] = Size.Fixed(widthNumSeqPlot)
axErrorbar = divider.new_horizontal(widthErrorBarPlot, pad=spacingBetweenPlots, sharey=axInitAxis)
self.fig.add_axes(axErrorbar)
else:
divider.get_horizontal()[0] = Size.Fixed(widthErrorBarPlot)
axErrorbar = axInitAxis
# *** Plot of sequences for each subsystem
if self.bShowBarPlot == True:
axNumSeq = axInitAxis
meanRelFreqSeqs1 = statsResults.getColumn('MeanRelFreq1')
meanRelFreqSeqs2 = statsResults.getColumn('MeanRelFreq2')
if self.bShowStdDev:
stdDev1 = statsResults.getColumn('StdDevRelFreq1')
stdDev2 = statsResults.getColumn('StdDevRelFreq2')
endCapSize = self.endCapSize
else:
stdDev1 = [0] * len(meanRelFreqSeqs1)
stdDev2 = [0] * len(meanRelFreqSeqs2)
endCapSize = 0
axNumSeq.barh(np.arange(len(features))+0.0, meanRelFreqSeqs1, height = 0.3, xerr=stdDev1, color=group1Colour, ecolor='black', capsize=endCapSize)
axNumSeq.barh(np.arange(len(features))-0.3, meanRelFreqSeqs2, height = 0.3, xerr=stdDev2, color=group2Colour, ecolor='black', capsize=endCapSize)
for value in np.arange(-0.5, len(features)-1, 2):
axNumSeq.axhspan(value, value+1, facecolor=highlightColor,edgecolor='none',zorder=-1)
axNumSeq.set_xlabel('Mean proportion (%)')
maxPercentage = max(max(meanRelFreqSeqs1), max(meanRelFreqSeqs2))
axNumSeq.set_xticks([0, maxPercentage])
axNumSeq.set_xlim([0, maxPercentage*1.05])
maxPercentageStr = '%.1f' % maxPercentage
axNumSeq.set_xticklabels(['0.0', maxPercentageStr])
axNumSeq.set_yticks(np.arange(len(features)))
axNumSeq.set_yticklabels(features)
axNumSeq.set_ylim([-1, len(features)])
for label in axNumSeq.get_yticklabels():
if label.get_text() in highlightedFeatures:
label.set_color('red')
for a in axNumSeq.yaxis.majorTicks:
a.tick1On=False
a.tick2On=False
for a in axNumSeq.xaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for line in axNumSeq.yaxis.get_ticklines():
line.set_color(axesColour)
for line in axNumSeq.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in axNumSeq.spines.iteritems():
if loc in ['left', 'right','top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
# *** Plot confidence intervals for each subsystem
lastAxes = axErrorbar
markerSize = math.sqrt(float(self.markerSize))
axErrorbar.errorbar(effectSizes, np.arange(len(features)), xerr=[lowerCIs,upperCIs], fmt='o', ms=markerSize, mfc=group1Colour, mec='black', ecolor='black', zorder=10)
effectSizesSample2 = [effectSizes[value] for value in dominateInSample2]
axErrorbar.plot(effectSizesSample2, dominateInSample2, ls='', marker='o', ms=markerSize, mfc=group2Colour, mec='black', zorder=100)
if statsResults.bConfIntervRatio:
axErrorbar.vlines(1, -1, len(features), linestyle='dashed', color=axesColour)
else:
axErrorbar.vlines(0, -1, len(features), linestyle='dashed', color=axesColour)
for value in np.arange(-0.5, len(features)-1, 2):
axErrorbar.axhspan(value, value+1, facecolor=highlightColor,edgecolor='none',zorder=1)
axErrorbar.set_title(ciTitle)
axErrorbar.set_xlabel('Difference in mean proportions (%)')
if self.bCustomLimits:
axErrorbar.set_xlim([self.minX, self.maxX])
else:
self.minX, self.maxX = axErrorbar.get_xlim()
if self.bShowBarPlot == False:
axErrorbar.set_yticks(np.arange(len(features)))
axErrorbar.set_yticklabels(features)
axErrorbar.set_ylim([-1, len(features)])
for label in axErrorbar.get_yticklabels():
if label.get_text() in self.preferences['Highlighted group features']:
label.set_color('red')
else:
for label in axErrorbar.get_yticklabels():
label.set_visible(False)
for a in axErrorbar.yaxis.majorTicks:
a.set_visible(False)
for a in axErrorbar.xaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for a in axErrorbar.yaxis.majorTicks:
a.tick1On=False
a.tick2On=False
for line in axErrorbar.yaxis.get_ticklines():
line.set_visible(False)
for line in axErrorbar.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in axErrorbar.spines.iteritems():
if loc in ['left','right','top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
# *** Show p-values on right of last plot
if self.bShowPValueLabels == True:
axRight = lastAxes.twinx()
axRight.set_yticks(np.arange(len(pValueLabels)))
axRight.set_yticklabels(pValueLabels)
axRight.set_ylim([-1, len(pValueLabels)])
axRight.set_ylabel(pValueTitle)
for a in axRight.yaxis.majorTicks:
a.tick1On=False
a.tick2On=False
# *** Legend
if self.legendPos != -1:
legend1 = Rectangle((0, 0), 1, 1, fc=group1Colour)
legend2 = Rectangle((0, 0), 1, 1, fc=group2Colour)
legend = self.fig.legend([legend1, legend2], (profile.groupName1, profile.groupName2), loc=self.legendPos, ncol=2)
legend.get_frame().set_linewidth(0)
self.updateGeometry()
self.draw()
def configure(self, profile, statsResults):
self.statsResults = statsResults
self.configDlg = ConfigureDialog(Ui_ExtendedErrorBarDialog)
# set enabled state of controls
self.configDlg.ui.chkShowStdDev.setChecked(self.bShowBarPlot)
self.configDlg.ui.spinEndCapSize.setValue(self.bShowBarPlot)
self.configDlg.ui.spinMinimumX.setEnabled(self.bCustomLimits)
self.configDlg.ui.spinMaximumX.setEnabled(self.bCustomLimits)
# set current value of controls
self.configDlg.ui.cboSortingField.setCurrentIndex(self.configDlg.ui.cboSortingField.findText(self.sortingField))
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigRowHeight.setValue(self.figHeightPerRow)
self.configDlg.ui.chkShowBarPlot.setChecked(self.bShowBarPlot)
self.configDlg.ui.chkPValueLabels.setChecked(self.bShowPValueLabels)
self.configDlg.ui.chkCorrectedPvalues.setChecked(self.bShowCorrectedPvalues)
self.configDlg.ui.chkCustomLimits.setChecked(self.bCustomLimits)
self.configDlg.ui.spinMinimumX.setValue(self.minX)
self.configDlg.ui.spinMaximumX.setValue(self.maxX)
self.configDlg.ui.spinMarkerSize.setValue(self.markerSize)
self.configDlg.ui.chkShowStdDev.setChecked(self.bShowStdDev)
self.configDlg.ui.spinEndCapSize.setValue(self.endCapSize)
if self.legendPos == 2:
self.configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 3:
self.configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
elif self.legendPos == 4:
self.configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 8:
self.configDlg.ui.radioLegendPosLowerCentre.setChecked(True)
else:
self.configDlg.ui.radioLegendPosNone.setChecked(True)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
QtGui.QApplication.instance().setOverrideCursor(QtGui.QCursor(QtCore.Qt.WaitCursor))
self.sortingField = str(self.configDlg.ui.cboSortingField.currentText())
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeightPerRow = self.configDlg.ui.spinFigRowHeight.value()
self.bShowBarPlot = self.configDlg.ui.chkShowBarPlot.isChecked()
self.bShowPValueLabels = self.configDlg.ui.chkPValueLabels.isChecked()
self.bShowCorrectedPvalues = self.configDlg.ui.chkCorrectedPvalues.isChecked()
self.bCustomLimits = self.configDlg.ui.chkCustomLimits.isChecked()
self.minX = self.configDlg.ui.spinMinimumX.value()
self.maxX = self.configDlg.ui.spinMaximumX.value()
self.markerSize = self.configDlg.ui.spinMarkerSize.value()
self.bShowStdDev = self.configDlg.ui.chkShowStdDev.isChecked()
self.endCapSize = self.configDlg.ui.spinEndCapSize.value()
# legend position
if self.configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif self.configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
elif self.configDlg.ui.radioLegendPosLowerCentre.isChecked() == True:
self.legendPos = 8
elif self.configDlg.ui.radioLegendPosLowerRight.isChecked() == True:
self.legendPos = 4
else:
self.legendPos = -1
self.settings.setValue('group: ' + self.name + '/width', self.figWidth)
self.settings.setValue('group: ' + self.name + '/row height', self.figHeightPerRow)
self.settings.setValue('group: ' + self.name + '/field', self.sortingField)
self.settings.setValue('group: ' + self.name + '/sequences subplot', self.bShowBarPlot)
self.settings.setValue('group: ' + self.name + '/p-value labels', self.bShowPValueLabels)
self.settings.setValue('group: ' + self.name + '/show corrected p-values', self.bShowCorrectedPvalues)
self.settings.setValue('group: ' + self.name + '/use custom limits', self.bCustomLimits)
self.settings.setValue('group: ' + self.name + '/minimum', self.minX)
self.settings.setValue('group: ' + self.name + '/maximum', self.maxX)
self.settings.setValue('group: ' + self.name + '/marker size', self.markerSize)
self.settings.setValue('group: ' + self.name + '/show std. dev.', self.bShowStdDev)
self.settings.setValue('group: ' + self.name + '/end cap size', self.endCapSize)
self.settings.setValue('group: ' + self.name + '/legend position', self.legendPos)
self.plot(profile, statsResults)
QtGui.QApplication.instance().restoreOverrideCursor()
def configure(self, profile, statsResults):
configDlg = ConfigureDialog(Ui_PcaPlotDialog)
configDlg.ui.spinFigWidth.setValue(self.figWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.chkFixedPixelsPerUnitDistance.setChecked(
self.bFixedPixelsPerUnitDistance)
configDlg.ui.spinFigHeight.setDisabled(
configDlg.ui.chkFixedPixelsPerUnitDistance.isChecked())
configDlg.ui.spinMarkerSize.setValue(self.markerSize)
configDlg.ui.chkRotateLabels.setChecked(self.bRotateLabels)
configDlg.ui.chkPC1vsPC3.setChecked(self.bShowPC1vsPC3)
configDlg.ui.chkPC3vsPC2.setChecked(self.bShowPC3vsPC2)
if self.legendPos == 2:
configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 3:
configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
elif self.legendPos == 4:
configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 9:
configDlg.ui.radioLegendPosUpperCentre.setChecked(True)
elif self.legendPos == 1:
configDlg.ui.radioLegendPosUpperRight.setChecked(True)
else:
configDlg.ui.radioLegendPosNone.setChecked(True)
configDlg.ui.chkUniqueShapes.setChecked(self.bUniqueShapes)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = configDlg.ui.spinFigWidth.value()
self.figHeight = configDlg.ui.spinFigHeight.value()
self.bFixedPixelsPerUnitDistance = configDlg.ui.chkFixedPixelsPerUnitDistance.isChecked(
)
self.markerSize = configDlg.ui.spinMarkerSize.value()
self.bRotateLabels = configDlg.ui.chkRotateLabels.isChecked()
self.bShowPC1vsPC3 = configDlg.ui.chkPC1vsPC3.isChecked()
self.bShowPC3vsPC2 = configDlg.ui.chkPC3vsPC2.isChecked()
# legend position
if configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
elif configDlg.ui.radioLegendPosUpperCentre.isChecked() == True:
self.legendPos = 9
elif configDlg.ui.radioLegendPosLowerRight.isChecked() == True:
self.legendPos = 4
elif configDlg.ui.radioLegendPosUpperRight.isChecked() == True:
self.legendPos = 1
else:
self.legendPos = -1
self.bUniqueShapes = configDlg.ui.chkUniqueShapes.isChecked()
self.settings.setValue('group: ' + self.name + '/width',
self.figWidth)
self.settings.setValue('group: ' + self.name + '/height',
self.figHeight)
self.settings.setValue(
'group: ' + self.name + '/fixed pixels per unit distance',
self.bFixedPixelsPerUnitDistance)
self.settings.setValue('group: ' + self.name + '/marker size',
self.markerSize)
self.settings.setValue(
'group: ' + self.name + '/rotate pc3 labels',
self.bRotateLabels)
self.settings.setValue('group: ' + self.name + '/showPC1vsPC3',
self.bShowPC1vsPC3)
self.settings.setValue('group: ' + self.name + '/showPC3vsPC2',
self.bShowPC3vsPC2)
self.settings.setValue('group: ' + self.name + '/legend position',
self.legendPos)
self.settings.setValue('group: ' + self.name + '/unique shapes',
self.bUniqueShapes)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
configDlg = ConfigureDialog(Ui_BarPlotDialog)
configDlg.ui.cboFieldToPlot.setCurrentIndex(
configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
configDlg.ui.spinFigColWidth.setValue(self.figColWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.chkShowAverage.setChecked(self.bShowAverages)
# legend position
if self.legendPos == 0:
configDlg.ui.radioLegendPosBest.setDown(True)
elif self.legendPos == 1:
configDlg.ui.radioLegendPosUpperRight.setChecked(True)
elif self.legendPos == 7:
configDlg.ui.radioLegendPosCentreRight.setChecked(True)
elif self.legendPos == 4:
configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 2:
configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 6:
configDlg.ui.radioLegendPosCentreLeft.setChecked(True)
elif self.legendPos == 3:
configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
else:
configDlg.ui.radioLegendPosNone.setChecked(True)
configDlg.ui.chkShowPvalue.setChecked(self.bShowPvalue)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.fieldToPlot = str(configDlg.ui.cboFieldToPlot.currentText())
self.figColWidth = configDlg.ui.spinFigColWidth.value()
self.figHeight = configDlg.ui.spinFigHeight.value()
self.bShowAverages = configDlg.ui.chkShowAverage.isChecked()
# legend position
if configDlg.ui.radioLegendPosBest.isChecked() == True:
self.legendPos = 0
elif configDlg.ui.radioLegendPosUpperRight.isChecked() == True:
self.legendPos = 1
elif configDlg.ui.radioLegendPosCentreRight.isChecked() == True:
self.legendPos = 7
elif configDlg.ui.radioLegendPosLowerRight.isChecked() == True:
self.legendPos = 4
elif configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif configDlg.ui.radioLegendPosCentreLeft.isChecked() == True:
self.legendPos = 6
elif configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
else:
self.legendPos = -1
self.bShowPvalue = configDlg.ui.chkShowPvalue.isChecked()
self.settings.setValue('group: ' + self.name + '/column width',
self.figColWidth)
self.settings.setValue('group: ' + self.name + '/height',
self.figHeight)
self.settings.setValue('group: ' + self.name + '/field to plot',
self.fieldToPlot)
self.settings.setValue('group: ' + self.name + '/show averages',
self.bShowAverages)
self.settings.setValue('group: ' + self.name + '/legend position',
self.legendPos)
self.settings.setValue('group: ' + self.name + '/show p-value',
self.bShowPvalue)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
configDlg = ConfigureDialog(Ui_HeatmapPlotDialog)
configDlg.ui.cboFieldToPlot.setCurrentIndex(configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
configDlg.ui.spinFigWidth.setValue(self.figWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.cboDendrogramMethod.setCurrentIndex(configDlg.ui.cboDendrogramMethod.findText(self.dendrogramMethod))
configDlg.ui.chkShowTopDendrogram.setChecked(self.bShowTopDendrogram)
configDlg.ui.chkShowLeftDendrogram.setChecked(self.bShowLeftDendrogram)
configDlg.ui.cboColourMap.setCurrentIndex(configDlg.ui.cboColourMap.findText(self.colourmap))
# legend position
if self.legendPos == 1:
configDlg.ui.radioLegendPosUpperRight.setChecked(True)
elif self.legendPos == 4:
configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 2:
configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 3:
configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
else:
configDlg.ui.radioLegendPosNone.setChecked(True)
configDlg.ui.spinClusteringThreshold.setValue(self.clusteringThreshold)
configDlg.ui.spinDendrogramWidth.setValue(self.dendrogramWidth)
configDlg.ui.spinDendrogramHeight.setValue(self.dendrogramHeight)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.fieldToPlot = str(configDlg.ui.cboFieldToPlot.currentText())
self.figWidth = configDlg.ui.spinFigWidth.value()
self.figHeight = configDlg.ui.spinFigHeight.value()
self.dendrogramMethod = str(configDlg.ui.cboDendrogramMethod.currentText())
self.bShowTopDendrogram = configDlg.ui.chkShowTopDendrogram.isChecked()
self.bShowLeftDendrogram = configDlg.ui.chkShowLeftDendrogram.isChecked()
self.colourmap = str(configDlg.ui.cboColourMap.currentText())
# legend position
if configDlg.ui.radioLegendPosUpperRight.isChecked() == True:
self.legendPos = 1
elif configDlg.ui.radioLegendPosLowerRight.isChecked() == True:
self.legendPos = 4
elif configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
else:
self.legendPos = -1
self.clusteringThreshold = configDlg.ui.spinClusteringThreshold.value()
self.dendrogramWidth = configDlg.ui.spinDendrogramWidth.value()
self.dendrogramHeight = configDlg.ui.spinDendrogramHeight.value()
self.settings.setValue('group: ' + self.name + '/field to plot', self.fieldToPlot)
self.settings.setValue('group: ' + self.name + '/width', self.figWidth)
self.settings.setValue('group: ' + self.name + '/height', self.figHeight)
self.settings.setValue('group: ' + self.name + '/dendrogram method', self.dendrogramMethod)
self.settings.setValue('group: ' + self.name + '/show top dendrogram', self.bShowTopDendrogram)
self.settings.setValue('group: ' + self.name + '/show left dendrogram', self.bShowLeftDendrogram)
self.settings.setValue('group: ' + self.name + '/colourmap', self.colourmap)
self.settings.setValue('group: ' + self.name + '/legend position', self.legendPos)
self.settings.setValue('group: ' + self.name + '/clustering threshold', self.clusteringThreshold)
self.settings.setValue('group: ' + self.name + '/dendrogram height', self.dendrogramHeight)
self.settings.setValue('group: ' + self.name + '/dendrogram width', self.dendrogramWidth)
self.plot(profile, statsResults)