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):
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_HeatmapPlotDialog)
configDlg.ui.cboFieldToPlot.setCurrentIndex(
configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
configDlg.ui.chkPlotOnlyActiveFeatures.setChecked(
self.bPlotOnlyActiveFeatures)
configDlg.ui.spinFigWidth.setValue(self.figWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.cboColSortMethod.setCurrentIndex(
configDlg.ui.cboColSortMethod.findText(self.sortColMethod))
configDlg.ui.cboRowSortMethod.setCurrentIndex(
configDlg.ui.cboRowSortMethod.findText(self.sortRowMethod))
configDlg.ui.chkShowColDendrogram.setChecked(self.bShowColDendrogram)
configDlg.ui.chkShowRowDendrogram.setChecked(self.bShowRowDendrogram)
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.spinColClusteringThreshold.setValue(
self.clusteringColThreshold)
configDlg.ui.spinRowClusteringThreshold.setValue(
self.clusteringRowThreshold)
configDlg.ui.spinDendrogramColHeight.setValue(self.dendrogramHeight)
configDlg.ui.spinDendrogramRowWidth.setValue(self.dendrogramWidth)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.fieldToPlot = str(configDlg.ui.cboFieldToPlot.currentText())
self.bPlotOnlyActiveFeatures = configDlg.ui.chkPlotOnlyActiveFeatures.isChecked(
)
self.figWidth = configDlg.ui.spinFigWidth.value()
self.figHeight = configDlg.ui.spinFigHeight.value()
self.sortColMethod = str(
configDlg.ui.cboColSortMethod.currentText())
self.sortRowMethod = str(
configDlg.ui.cboRowSortMethod.currentText())
self.bShowColDendrogram = configDlg.ui.chkShowColDendrogram.isChecked(
)
self.bShowRowDendrogram = configDlg.ui.chkShowRowDendrogram.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.clusteringColThreshold = configDlg.ui.spinColClusteringThreshold.value(
)
self.clusteringRowThreshold = configDlg.ui.spinRowClusteringThreshold.value(
)
self.dendrogramHeight = configDlg.ui.spinDendrogramColHeight.value(
)
self.dendrogramWidth = configDlg.ui.spinDendrogramRowWidth.value()
self.settings.setValue('group: ' + self.name + '/field to plot',
self.fieldToPlot)
self.settings.setValue(
'group: ' + self.name + '/plot only active features',
self.bPlotOnlyActiveFeatures)
self.settings.setValue('group: ' + self.name + '/width',
self.figWidth)
self.settings.setValue('group: ' + self.name + '/height',
self.figHeight)
self.settings.setValue('group: ' + self.name + '/sort col method',
self.sortColMethod)
self.settings.setValue('group: ' + self.name + '/sort row method',
self.sortRowMethod)
self.settings.setValue(
'group: ' + self.name + '/show col dendrogram',
self.bShowColDendrogram)
self.settings.setValue(
'group: ' + self.name + '/show row dendrogram',
self.bShowRowDendrogram)
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 col threshold',
self.clusteringColThreshold)
self.settings.setValue(
'group: ' + self.name + '/clustering row threshold',
self.clusteringRowThreshold)
self.settings.setValue(
'group: ' + self.name + '/dendrogram col height',
self.dendrogramHeight)
self.settings.setValue(
'group: ' + self.name + '/dendrogram row width',
self.dendrogramWidth)
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_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)
