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('multiple group: ' + self.name + '/column width', self.figWidth)
self.settings.setValue('multiple group: ' + self.name + '/height', self.figHeight)
self.settings.setValue('multiple group: ' + self.name + '/field to plot', self.fieldToPlot)
self.settings.setValue('multiple group: ' + self.name + '/show averages', self.bShowAverages)
self.settings.setValue('multiple 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)
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()
self.bUniqueShapes = configDlg.ui.chkUniqueShapes.isChecked()
self.settings.setValue("multiple group: " + self.name + "/width", self.figWidth)
self.settings.setValue("multiple group: " + self.name + "/height", self.figHeight)
self.settings.setValue(
"multiple group: " + self.name + "/fixed pixels per unit distance", self.bFixedPixelsPerUnitDistance
)
self.settings.setValue("multiple group: " + self.name + "/marker size", self.markerSize)
self.settings.setValue("multiple group: " + self.name + "/rotate pc3 labels", self.bRotateLabels)
self.settings.setValue("multiple group: " + self.name + "/showPC1vsPC3", self.bShowPC1vsPC3)
self.settings.setValue("multiple group: " + self.name + "/showPC3vsPC2", self.bShowPC3vsPC2)
self.settings.setValue("group: " + self.name + "/unique shapes", self.bUniqueShapes)
self.plot(profile, statsResults)
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(
'multiple group: ' + self.name + '/column width',
self.figWidth)
self.settings.setValue('multiple group: ' + self.name + '/height',
self.figHeight)
self.settings.setValue(
'multiple group: ' + self.name + '/field to plot',
self.fieldToPlot)
self.settings.setValue(
'multiple group: ' + self.name + '/show averages',
self.bShowAverages)
self.settings.setValue(
'multiple group: ' + self.name + '/show p-value',
self.bShowPvalue)
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('multiple group: ' + self.name + '/column width', self.figColWidth)
self.settings.setValue('multiple group: ' + self.name + '/height', self.figHeight)
self.settings.setValue('multiple group: ' + self.name + '/field to plot', self.fieldToPlot)
self.settings.setValue('multiple group: ' + self.name + '/show averages', self.bShowAverages)
self.settings.setValue('multiple group: ' + self.name + '/legend position', self.legendPos)
self.settings.setValue('multiple 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)
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()
self.bUniqueShapes = configDlg.ui.chkUniqueShapes.isChecked()
self.settings.setValue('multiple group: ' + self.name + '/width',
self.figWidth)
self.settings.setValue('multiple group: ' + self.name + '/height',
self.figHeight)
self.settings.setValue(
'multiple group: ' + self.name +
'/fixed pixels per unit distance',
self.bFixedPixelsPerUnitDistance)
self.settings.setValue(
'multiple group: ' + self.name + '/marker size',
self.markerSize)
self.settings.setValue(
'multiple group: ' + self.name + '/rotate pc3 labels',
self.bRotateLabels)
self.settings.setValue(
'multiple group: ' + self.name + '/showPC1vsPC3',
self.bShowPC1vsPC3)
self.settings.setValue(
'multiple group: ' + self.name + '/showPC3vsPC2',
self.bShowPC3vsPC2)
self.settings.setValue('group: ' + self.name + '/unique shapes',
self.bUniqueShapes)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
self.configDlg = ConfigureDialog(Ui_PostHocPlotDialog)
# 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.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)
self.configDlg.ui.chkFilterPvalue.setChecked(self.bPvalueFilter)
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.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()
self.bPvalueFilter = self.configDlg.ui.chkFilterPvalue.isChecked()
self.settings.setValue('multiple group: ' + self.name + '/width', self.figWidth)
self.settings.setValue('multiple group: ' + self.name + '/row height', self.figHeightPerRow)
self.settings.setValue('multiple group: ' + self.name + '/field', self.sortingField)
self.settings.setValue('multiple group: ' + self.name + '/sequences subplot', self.bShowBarPlot)
self.settings.setValue('multiple group: ' + self.name + '/p-value labels', self.bShowPValueLabels)
self.settings.setValue('multiple group: ' + self.name + '/use custom limits', self.bCustomLimits)
self.settings.setValue('multiple group: ' + self.name + '/minimum', self.minX)
self.settings.setValue('multiple group: ' + self.name + '/maximum', self.maxX)
self.settings.setValue('multiple group: ' + self.name + '/marker size', self.markerSize)
self.settings.setValue('multiple group: ' + self.name + '/show std. dev.', self.bShowStdDev)
self.settings.setValue('multiple group: ' + self.name + '/end cap size', self.endCapSize)
self.settings.setValue('multiple group: ' + self.name + '/p-value filter', self.bPvalueFilter)
self.plot(profile, statsResults)
QtGui.QApplication.instance().restoreOverrideCursor()
class PostHocPlot(AbstractMultiGroupPlotPlugin):
'''
Post-hoc plot.
'''
def __init__(self, preferences, parent=None):
AbstractMultiGroupPlotPlugin.__init__(self, preferences, parent)
self.name = 'Post-hoc plot'
self.type = 'Statistical'
self.bRunPostHocTest = True
self.settings = preferences['Settings']
self.figWidth = self.settings.value('multiple group: ' + self.name + '/width', 7.0).toDouble()[0]
self.figHeightPerRow = self.settings.value('multiple group: ' + self.name + '/row height', 0.2).toDouble()[0]
self.sortingField = self.settings.value('multiple group: ' + self.name + '/field', 'p-values').toString()
self.bShowBarPlot = self.settings.value('multiple group: ' + self.name + '/sequences subplot', True).toBool()
self.bShowPValueLabels = self.settings.value('multiple group: ' + self.name + '/p-value labels', True).toBool()
self.bCustomLimits = self.settings.value('multiple group: ' + self.name + '/use custom limits', False).toBool()
self.minX = self.settings.value('multiple group: ' + self.name + '/minimum', 0.0).toDouble()[0]
self.maxX = self.settings.value('multiple group: ' + self.name + '/maximum', 1.0).toDouble()[0]
self.markerSize = self.settings.value('multiple group: ' + self.name + '/marker size', 30).toInt()[0]
self.bShowStdDev = self.settings.value('multiple group: ' + self.name + '/show std. dev.', False).toBool()
self.endCapSize = self.settings.value('multiple group: ' + self.name + '/end cap size', 0.0).toInt()[0]
self.bPvalueFilter = self.settings.value('multiple group: ' + self.name + '/p-value filter', True).toBool()
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.bCustomLimits = plotToCopy.bCustomLimits
self.minX = plotToCopy.minX
self.maxX = plotToCopy.maxX
self.markerSize = plotToCopy.markerSize
self.bShowStdDev = plotToCopy.bShowStdDev
self.endCapSize = plotToCopy.endCapSize
self.bPvalueFilter = plotToCopy.bPvalueFilter
def plot(self, profile, statsResults):
# *** Check if there is sufficient data to generate the plot
if len(statsResults.postHocResults.pValues) <= 0:
self.emptyAxis('No post-hoc test results')
return
if len(statsResults.postHocResults.pValues) > 200:
QtGui.QApplication.instance().setOverrideCursor(QtGui.QCursor(QtCore.Qt.ArrowCursor))
reply = QtGui.QMessageBox.question(self, 'Continue?', 'Plots contains ' + str(len(statsResults.postHocResults.pValues)) + ' rows. ' +
'It may take several seconds to generate this plot. We recommend filtering the results first.' +
'Do you wish to continue?', QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
QtGui.QApplication.instance().restoreOverrideCursor()
if reply == QtGui.QMessageBox.No:
self.emptyAxis('Too many rows.')
return
# *** Set plot properties
axesColour = str(self.preferences['Axes colour'].name())
highlightColor = (0.9, 0.9, 0.9)
# Apply p-value filter
labels = []
pValues = []
effectSizes = []
lowerCIs = []
upperCIs = []
if self.bPvalueFilter:
for i in xrange(0, len(statsResults.postHocResults.labels)):
# get numeric p-value
if isinstance(statsResults.postHocResults.pValues[i], str):
pValueSplit = statsResults.postHocResults.pValues[i].split(' ')
if pValueSplit[0][0] == '<':
pValue = float(pValueSplit[1]) - 1e-6
else:
pValue = 1.0
else:
pValue = statsResults.postHocResults.pValues[i]
# check if p-value should be filtered
if pValue <= statsResults.postHocResults.alpha:
labels.append(statsResults.postHocResults.labels[i])
pValues.append(statsResults.postHocResults.pValues[i])
effectSizes.append(statsResults.postHocResults.effectSizes[i])
lowerCIs.append(statsResults.postHocResults.lowerCIs[i])
upperCIs.append(statsResults.postHocResults.upperCIs[i])
else:
labels = list(statsResults.postHocResults.labels)
pValues = list(statsResults.postHocResults.pValues)
effectSizes = list(statsResults.postHocResults.effectSizes)
lowerCIs = list(statsResults.postHocResults.lowerCIs)
upperCIs = list(statsResults.postHocResults.upperCIs)
if len(labels) == 0:
self.emptyAxis('No rows above nominal level.')
return
# *** Determine dominant group for each contrast (i.e., row).
# Adjust labels and effect sizes to reflect the dominant group.
for i in xrange(0, len(effectSizes)):
labelSplit = labels[i].split(':')
if effectSizes[i] > 0.0:
lowerCIs[i] = effectSizes[i] - lowerCIs[i]
upperCIs[i] = upperCIs[i] - effectSizes[i]
else:
labels[i] = labelSplit[1].strip() + ' : ' + labelSplit[0].strip()
lowerCIs[i] = effectSizes[i] - lowerCIs[i]
upperCIs[i] = upperCIs[i] - effectSizes[i]
effectSizes[i] = -effectSizes[i]
# *** Sort data
data = zip(labels, pValues, effectSizes, lowerCIs, upperCIs)
if self.sortingField == 'p-values':
data = sorted(data, key = operator.itemgetter(1), reverse = True)
elif self.sortingField == 'Effect sizes':
data = sorted(data, key = operator.itemgetter(2))
elif self.sortingField == 'Group labels':
data = sorted(data, key = lambda row: row[0].lower(), reverse = True)
labels, pValues, effectSizes, lowerCIs, upperCIs = zip(*data)
labels = list(labels)
pValues = list(pValues)
effectSizes = list(effectSizes)
lowerCIs = list(lowerCIs)
upperCIs = list(upperCIs)
# *** Make list of which group is dominant in each contrast.
dominantGroup = {}
for i in xrange(0, len(effectSizes)):
labelSplit = labels[i].split(':')
groupName = labelSplit[0].strip()
if groupName in dominantGroup:
dominantGroup[groupName][0].append(effectSizes[i])
dominantGroup[groupName][1].append(i)
else:
dominantGroup[groupName] = [[effectSizes[i]],[i]]
# *** Create p-value labels
pValueTitle = 'p-value'
pValueLabels = []
for pValue in pValues:
if isinstance(pValue, str):
pValueSplit = pValue.split(' ')
if pValue[0] == '<':
pValueLabels.append(r'$<$' + pValueSplit[1])
else:
pValueLabels.append(r'$\geq$' + pValueSplit[1])
else:
pValueLabels.append(statsResults.getPValueStr(pValue))
# *** Truncate labels
adjustedLabels = list(labels)
if self.preferences['Truncate feature names']:
length = self.preferences['Length of truncated feature names']
for i in xrange(0, len(labels)):
if len(labels[i]) > length+3:
adjustedLabels[i] = labels[i][0:length] + '...'
# *** Set figure size
plotHeight = self.figHeightPerRow*len(adjustedLabels)
self.imageWidth = self.figWidth
self.imageHeight = plotHeight + 0.65 # 0.65 inches for bottom and top labels
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(adjustedLabels, 8)
# *** Size plots which comprise the extended errorbar plot
self.fig.clear()
heightBottomLabels = 0.4 # inches
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(labels)*self.figHeightPerRow)
self.fig.text(0.0,1.0,self.preferences['Selected multiple group feature'], va='top', ha='left')
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
# get relative frequency and standard deviation of each contrast
maxPercentage = 0
for i in xrange(0, len(labels)):
splitLabel = labels[i].split(':')
groupName1 = splitLabel[0].strip()
groupName2 = splitLabel[1].strip()
colour1 = str(self.preferences['Group colours'][groupName1].name())
colour2 = str(self.preferences['Group colours'][groupName2].name())
meanRelFreq1 = statsResults.getDataFromTable(statsResults.postHocResults.feature, groupName1 + ': mean rel. freq. (%)')
meanRelFreq2 = statsResults.getDataFromTable(statsResults.postHocResults.feature, groupName2 + ': mean rel. freq. (%)')
if self.bShowStdDev:
stdDev1 = statsResults.getDataFromTable(statsResults.postHocResults.feature, groupName1 + ': std. dev. (%)')
stdDev2 = statsResults.getDataFromTable(statsResults.postHocResults.feature, groupName2 + ': std. dev. (%)')
endCapSize = self.endCapSize
else:
stdDev1 = 0
stdDev2 = 0
endCapSize = 0
if meanRelFreq1 + stdDev1 > maxPercentage:
maxPercentage = meanRelFreq1 + stdDev1
if meanRelFreq2 + stdDev2 > maxPercentage:
maxPercentage = meanRelFreq2 + stdDev2
axNumSeq.barh(i+0.0, meanRelFreq1, height = 0.3, xerr=stdDev1, color=colour1, ecolor='black', capsize=endCapSize)
axNumSeq.barh(i-0.3, meanRelFreq2, height = 0.3, xerr=stdDev2, color=colour2, ecolor='black', capsize=endCapSize)
for value in np.arange(-0.5, len(labels)-1, 2):
axNumSeq.axhspan(value, value+1, facecolor=highlightColor, edgecolor='none', zorder=-1)
axNumSeq.set_xlabel('Mean proportion (%)')
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(labels)))
axNumSeq.set_yticklabels(adjustedLabels)
axNumSeq.set_ylim([-1, len(labels)])
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(labels)), xerr=[lowerCIs,upperCIs], fmt='o', ms=markerSize, mfc='black', mec='black', ecolor='black', zorder=10)
for groupName in dominantGroup:
colour = str(self.preferences['Group colours'][groupName].name())
effectSizes = dominantGroup[groupName][0]
indices = dominantGroup[groupName][1]
axErrorbar.plot(effectSizes, indices, ls='', marker='o', ms=markerSize, mfc=colour, mec='black', zorder=100)
axErrorbar.vlines(0, -1, len(labels), linestyle='dashed', color=axesColour)
for value in np.arange(-0.5, len(labels)-1, 2):
axErrorbar.axhspan(value, value+1, facecolor=highlightColor,edgecolor='none',zorder=1)
ciTitle = ('%.3g' % ((1.0-statsResults.postHocResults.alpha)*100)) + '% confidence intervals'
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(labels)))
axErrorbar.set_yticklabels(labels)
axErrorbar.set_ylim([-1, len(labels)])
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
self.updateGeometry()
self.draw()
def configure(self, profile, statsResults):
self.configDlg = ConfigureDialog(Ui_PostHocPlotDialog)
# 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.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)
self.configDlg.ui.chkFilterPvalue.setChecked(self.bPvalueFilter)
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.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()
self.bPvalueFilter = self.configDlg.ui.chkFilterPvalue.isChecked()
self.settings.setValue('multiple group: ' + self.name + '/width', self.figWidth)
self.settings.setValue('multiple group: ' + self.name + '/row height', self.figHeightPerRow)
self.settings.setValue('multiple group: ' + self.name + '/field', self.sortingField)
self.settings.setValue('multiple group: ' + self.name + '/sequences subplot', self.bShowBarPlot)
self.settings.setValue('multiple group: ' + self.name + '/p-value labels', self.bShowPValueLabels)
self.settings.setValue('multiple group: ' + self.name + '/use custom limits', self.bCustomLimits)
self.settings.setValue('multiple group: ' + self.name + '/minimum', self.minX)
self.settings.setValue('multiple group: ' + self.name + '/maximum', self.maxX)
self.settings.setValue('multiple group: ' + self.name + '/marker size', self.markerSize)
self.settings.setValue('multiple group: ' + self.name + '/show std. dev.', self.bShowStdDev)
self.settings.setValue('multiple group: ' + self.name + '/end cap size', self.endCapSize)
self.settings.setValue('multiple group: ' + self.name + '/p-value filter', self.bPvalueFilter)
self.plot(profile, statsResults)
QtGui.QApplication.instance().restoreOverrideCursor()
def configure(self, profile, statsResults):
self.configDlg = ConfigureDialog(Ui_PostHocPlotDialog)
# 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.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)
self.configDlg.ui.chkFilterPvalue.setChecked(self.bPvalueFilter)
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.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()
self.bPvalueFilter = self.configDlg.ui.chkFilterPvalue.isChecked()
self.settings.setValue('multiple group: ' + self.name + '/width',
self.figWidth)
self.settings.setValue(
'multiple group: ' + self.name + '/row height',
self.figHeightPerRow)
self.settings.setValue('multiple group: ' + self.name + '/field',
self.sortingField)
self.settings.setValue(
'multiple group: ' + self.name + '/sequences subplot',
self.bShowBarPlot)
self.settings.setValue(
'multiple group: ' + self.name + '/p-value labels',
self.bShowPValueLabels)
self.settings.setValue(
'multiple group: ' + self.name + '/use custom limits',
self.bCustomLimits)
self.settings.setValue('multiple group: ' + self.name + '/minimum',
self.minX)
self.settings.setValue('multiple group: ' + self.name + '/maximum',
self.maxX)
self.settings.setValue(
'multiple group: ' + self.name + '/marker size',
self.markerSize)
self.settings.setValue(
'multiple group: ' + self.name + '/show std. dev.',
self.bShowStdDev)
self.settings.setValue(
'multiple group: ' + self.name + '/end cap size',
self.endCapSize)
self.settings.setValue(
'multiple group: ' + self.name + '/p-value filter',
self.bPvalueFilter)
self.plot(profile, statsResults)
QtGui.QApplication.instance().restoreOverrideCursor()
class PostHocPlot(AbstractMultiGroupPlotPlugin):
'''
Post-hoc plot.
'''
def __init__(self, preferences, parent=None):
AbstractMultiGroupPlotPlugin.__init__(self, preferences, parent)
self.name = 'Post-hoc plot'
self.type = 'Statistical'
self.bRunPostHocTest = True
self.settings = preferences['Settings']
self.figWidth = self.settings.value(
'multiple group: ' + self.name + '/width', 7.0).toDouble()[0]
self.figHeightPerRow = self.settings.value(
'multiple group: ' + self.name + '/row height', 0.2).toDouble()[0]
self.sortingField = self.settings.value(
'multiple group: ' + self.name + '/field', 'p-values').toString()
self.bShowBarPlot = self.settings.value(
'multiple group: ' + self.name + '/sequences subplot',
True).toBool()
self.bShowPValueLabels = self.settings.value(
'multiple group: ' + self.name + '/p-value labels', True).toBool()
self.bCustomLimits = self.settings.value(
'multiple group: ' + self.name + '/use custom limits',
False).toBool()
self.minX = self.settings.value(
'multiple group: ' + self.name + '/minimum', 0.0).toDouble()[0]
self.maxX = self.settings.value(
'multiple group: ' + self.name + '/maximum', 1.0).toDouble()[0]
self.markerSize = self.settings.value(
'multiple group: ' + self.name + '/marker size', 30).toInt()[0]
self.bShowStdDev = self.settings.value(
'multiple group: ' + self.name + '/show std. dev.',
False).toBool()
self.endCapSize = self.settings.value(
'multiple group: ' + self.name + '/end cap size', 0.0).toInt()[0]
self.bPvalueFilter = self.settings.value(
'multiple group: ' + self.name + '/p-value filter', True).toBool()
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.bCustomLimits = plotToCopy.bCustomLimits
self.minX = plotToCopy.minX
self.maxX = plotToCopy.maxX
self.markerSize = plotToCopy.markerSize
self.bShowStdDev = plotToCopy.bShowStdDev
self.endCapSize = plotToCopy.endCapSize
self.bPvalueFilter = plotToCopy.bPvalueFilter
def plot(self, profile, statsResults):
# *** Check if there is sufficient data to generate the plot
if len(statsResults.postHocResults.pValues) <= 0:
self.emptyAxis('No post-hoc test results')
return
if len(statsResults.postHocResults.pValues) > 200:
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.ArrowCursor))
reply = QtGui.QMessageBox.question(
self, 'Continue?', 'Plots contains ' +
str(len(statsResults.postHocResults.pValues)) + ' rows. ' +
'It may take several seconds to generate this plot. We recommend filtering the results first.'
+ 'Do you wish to continue?', QtGui.QMessageBox.Yes,
QtGui.QMessageBox.No)
QtGui.QApplication.instance().restoreOverrideCursor()
if reply == QtGui.QMessageBox.No:
self.emptyAxis('Too many rows.')
return
# *** Set plot properties
axesColour = str(self.preferences['Axes colour'].name())
highlightColor = (0.9, 0.9, 0.9)
# Apply p-value filter
labels = []
pValues = []
effectSizes = []
lowerCIs = []
upperCIs = []
if self.bPvalueFilter:
for i in xrange(0, len(statsResults.postHocResults.labels)):
# get numeric p-value
if isinstance(statsResults.postHocResults.pValues[i], str):
pValueSplit = statsResults.postHocResults.pValues[i].split(
' ')
if pValueSplit[0][0] == '<':
pValue = float(pValueSplit[1]) - 1e-6
else:
pValue = 1.0
else:
pValue = statsResults.postHocResults.pValues[i]
# check if p-value should be filtered
if pValue <= statsResults.postHocResults.alpha:
labels.append(statsResults.postHocResults.labels[i])
pValues.append(statsResults.postHocResults.pValues[i])
effectSizes.append(
statsResults.postHocResults.effectSizes[i])
lowerCIs.append(statsResults.postHocResults.lowerCIs[i])
upperCIs.append(statsResults.postHocResults.upperCIs[i])
else:
labels = list(statsResults.postHocResults.labels)
pValues = list(statsResults.postHocResults.pValues)
effectSizes = list(statsResults.postHocResults.effectSizes)
lowerCIs = list(statsResults.postHocResults.lowerCIs)
upperCIs = list(statsResults.postHocResults.upperCIs)
if len(labels) == 0:
self.emptyAxis('No rows above nominal level.')
return
# *** Determine dominant group for each contrast (i.e., row).
# Adjust labels and effect sizes to reflect the dominant group.
for i in xrange(0, len(effectSizes)):
labelSplit = labels[i].split(':')
if effectSizes[i] > 0.0:
lowerCIs[i] = effectSizes[i] - lowerCIs[i]
upperCIs[i] = upperCIs[i] - effectSizes[i]
else:
labels[i] = labelSplit[1].strip(
) + ' : ' + labelSplit[0].strip()
lowerCIs[i] = effectSizes[i] - lowerCIs[i]
upperCIs[i] = upperCIs[i] - effectSizes[i]
effectSizes[i] = -effectSizes[i]
# *** Sort data
data = zip(labels, pValues, effectSizes, lowerCIs, upperCIs)
if self.sortingField == 'p-values':
data = sorted(data, key=operator.itemgetter(1), reverse=True)
elif self.sortingField == 'Effect sizes':
data = sorted(data, key=operator.itemgetter(2))
elif self.sortingField == 'Group labels':
data = sorted(data, key=lambda row: row[0].lower(), reverse=True)
labels, pValues, effectSizes, lowerCIs, upperCIs = zip(*data)
labels = list(labels)
pValues = list(pValues)
effectSizes = list(effectSizes)
lowerCIs = list(lowerCIs)
upperCIs = list(upperCIs)
# *** Make list of which group is dominant in each contrast.
dominantGroup = {}
for i in xrange(0, len(effectSizes)):
labelSplit = labels[i].split(':')
groupName = labelSplit[0].strip()
if groupName in dominantGroup:
dominantGroup[groupName][0].append(effectSizes[i])
dominantGroup[groupName][1].append(i)
else:
dominantGroup[groupName] = [[effectSizes[i]], [i]]
# *** Create p-value labels
pValueTitle = 'p-value'
pValueLabels = []
for pValue in pValues:
if isinstance(pValue, str):
pValueSplit = pValue.split(' ')
if pValue[0] == '<':
pValueLabels.append(r'$<$' + pValueSplit[1])
else:
pValueLabels.append(r'$\geq$' + pValueSplit[1])
else:
pValueLabels.append(statsResults.getPValueStr(pValue))
# *** Truncate labels
adjustedLabels = list(labels)
if self.preferences['Truncate feature names']:
length = self.preferences['Length of truncated feature names']
for i in xrange(0, len(labels)):
if len(labels[i]) > length + 3:
adjustedLabels[i] = labels[i][0:length] + '...'
# *** Set figure size
plotHeight = self.figHeightPerRow * len(adjustedLabels)
self.imageWidth = self.figWidth
self.imageHeight = plotHeight + 0.65 # 0.65 inches for bottom and top labels
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(adjustedLabels, 8)
# *** Size plots which comprise the extended errorbar plot
self.fig.clear()
heightBottomLabels = 0.4 # inches
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(labels) * self.figHeightPerRow)
self.fig.text(0.0,
1.0,
self.preferences['Selected multiple group feature'],
va='top',
ha='left')
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
# get relative frequency and standard deviation of each contrast
maxPercentage = 0
for i in xrange(0, len(labels)):
splitLabel = labels[i].split(':')
groupName1 = splitLabel[0].strip()
groupName2 = splitLabel[1].strip()
colour1 = str(
self.preferences['Group colours'][groupName1].name())
colour2 = str(
self.preferences['Group colours'][groupName2].name())
meanRelFreq1 = statsResults.getDataFromTable(
statsResults.postHocResults.feature,
groupName1 + ': mean rel. freq. (%)')
meanRelFreq2 = statsResults.getDataFromTable(
statsResults.postHocResults.feature,
groupName2 + ': mean rel. freq. (%)')
if self.bShowStdDev:
stdDev1 = statsResults.getDataFromTable(
statsResults.postHocResults.feature,
groupName1 + ': std. dev. (%)')
stdDev2 = statsResults.getDataFromTable(
statsResults.postHocResults.feature,
groupName2 + ': std. dev. (%)')
endCapSize = self.endCapSize
else:
stdDev1 = 0
stdDev2 = 0
endCapSize = 0
if meanRelFreq1 + stdDev1 > maxPercentage:
maxPercentage = meanRelFreq1 + stdDev1
if meanRelFreq2 + stdDev2 > maxPercentage:
maxPercentage = meanRelFreq2 + stdDev2
axNumSeq.barh(i + 0.0,
meanRelFreq1,
height=0.3,
xerr=stdDev1,
color=colour1,
ecolor='black',
capsize=endCapSize)
axNumSeq.barh(i - 0.3,
meanRelFreq2,
height=0.3,
xerr=stdDev2,
color=colour2,
ecolor='black',
capsize=endCapSize)
for value in np.arange(-0.5, len(labels) - 1, 2):
axNumSeq.axhspan(value,
value + 1,
facecolor=highlightColor,
edgecolor='none',
zorder=-1)
axNumSeq.set_xlabel('Mean proportion (%)')
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(labels)))
axNumSeq.set_yticklabels(adjustedLabels)
axNumSeq.set_ylim([-1, len(labels)])
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(labels)),
xerr=[lowerCIs, upperCIs],
fmt='o',
ms=markerSize,
mfc='black',
mec='black',
ecolor='black',
zorder=10)
for groupName in dominantGroup:
colour = str(self.preferences['Group colours'][groupName].name())
effectSizes = dominantGroup[groupName][0]
indices = dominantGroup[groupName][1]
axErrorbar.plot(effectSizes,
indices,
ls='',
marker='o',
ms=markerSize,
mfc=colour,
mec='black',
zorder=100)
axErrorbar.vlines(0,
-1,
len(labels),
linestyle='dashed',
color=axesColour)
for value in np.arange(-0.5, len(labels) - 1, 2):
axErrorbar.axhspan(value,
value + 1,
facecolor=highlightColor,
edgecolor='none',
zorder=1)
ciTitle = ('%.3g' % ((1.0 - statsResults.postHocResults.alpha) * 100)
) + '% confidence intervals'
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(labels)))
axErrorbar.set_yticklabels(labels)
axErrorbar.set_ylim([-1, len(labels)])
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
self.updateGeometry()
self.draw()
def configure(self, profile, statsResults):
self.configDlg = ConfigureDialog(Ui_PostHocPlotDialog)
# 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.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)
self.configDlg.ui.chkFilterPvalue.setChecked(self.bPvalueFilter)
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.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()
self.bPvalueFilter = self.configDlg.ui.chkFilterPvalue.isChecked()
self.settings.setValue('multiple group: ' + self.name + '/width',
self.figWidth)
self.settings.setValue(
'multiple group: ' + self.name + '/row height',
self.figHeightPerRow)
self.settings.setValue('multiple group: ' + self.name + '/field',
self.sortingField)
self.settings.setValue(
'multiple group: ' + self.name + '/sequences subplot',
self.bShowBarPlot)
self.settings.setValue(
'multiple group: ' + self.name + '/p-value labels',
self.bShowPValueLabels)
self.settings.setValue(
'multiple group: ' + self.name + '/use custom limits',
self.bCustomLimits)
self.settings.setValue('multiple group: ' + self.name + '/minimum',
self.minX)
self.settings.setValue('multiple group: ' + self.name + '/maximum',
self.maxX)
self.settings.setValue(
'multiple group: ' + self.name + '/marker size',
self.markerSize)
self.settings.setValue(
'multiple group: ' + self.name + '/show std. dev.',
self.bShowStdDev)
self.settings.setValue(
'multiple group: ' + self.name + '/end cap size',
self.endCapSize)
self.settings.setValue(
'multiple group: ' + self.name + '/p-value filter',
self.bPvalueFilter)
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(
'multiple group: ' + self.name + '/column width',
self.figColWidth)
self.settings.setValue('multiple group: ' + self.name + '/height',
self.figHeight)
self.settings.setValue(
'multiple group: ' + self.name + '/field to plot',
self.fieldToPlot)
self.settings.setValue(
'multiple group: ' + self.name + '/show averages',
self.bShowAverages)
self.settings.setValue(
'multiple group: ' + self.name + '/legend position',
self.legendPos)
self.settings.setValue(
'multiple 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('multiple group: ' + self.name + '/field to plot', self.fieldToPlot)
self.settings.setValue('multiple group: ' + self.name + '/width', self.figWidth)
self.settings.setValue('multiple group: ' + self.name + '/height', self.figHeight)
self.settings.setValue('multiple group: ' + self.name + '/dendrogram method', self.dendrogramMethod)
self.settings.setValue('multiple group: ' + self.name + '/show top dendrogram', self.bShowTopDendrogram)
self.settings.setValue('multiple group: ' + self.name + '/show left dendrogram', self.bShowLeftDendrogram)
self.settings.setValue('multiple group: ' + self.name + '/colourmap', self.colourmap)
self.settings.setValue('multiple group: ' + self.name + '/legend position', self.legendPos)
self.settings.setValue('multiple group: ' + self.name + '/clustering threshold', self.clusteringThreshold)
self.settings.setValue('multiple group: ' + self.name + '/dendrogram height', self.dendrogramHeight)
self.settings.setValue('multiple group: ' + self.name + '/dendrogram width', self.dendrogramWidth)
self.plot(profile, statsResults)
