def configure(self, profile, statsResults):
self.configDlg = ConfigureDialog(Ui_MultCompCorrectionDialog)
self.connect(self.configDlg.ui.btnXmaxFig1, QtCore.SIGNAL('clicked()'),
self.setXaxisMax1)
self.connect(self.configDlg.ui.btnXmaxFig2, QtCore.SIGNAL('clicked()'),
self.setXaxisMax2)
self.connect(self.configDlg.ui.btnXmaxFig3, QtCore.SIGNAL('clicked()'),
self.setXaxisMax3)
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.spinXlimitFig1.setValue(self.xLimitFig1)
self.configDlg.ui.spinXlimitFig2.setValue(self.xLimitFig2)
self.configDlg.ui.spinXlimitFig3.setValue(self.xLimitFig3)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.xLimitFig1 = self.configDlg.ui.spinXlimitFig1.value()
self.xLimitFig2 = self.configDlg.ui.spinXlimitFig2.value()
self.xLimitFig3 = self.configDlg.ui.spinXlimitFig3.value()
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/histogram log scale',
self.yAxisLogScale)
self.settings.setValue(self.name + '/bin width', self.binWidth)
self.settings.setValue(self.name + '/histogram x-axis limit',
self.xLimitFig1)
self.settings.setValue(self.name + '/correction plot x-axis limit',
self.xLimitFig2)
self.settings.setValue(
self.name + '/significant features x-axis limit',
self.xLimitFig3)
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.chkShowCIs.setChecked(self.bShowCIs) 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.bShowCIs = configDlg.ui.chkShowCIs.isChecked() 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(self.name + '/width', self.figWidth) self.settings.setValue(self.name + '/height', self.figHeight) self.settings.setValue(self.name + '/show CIs', self.bShowCIs) self.settings.setValue(self.name + '/bin', self.numBins) self.settings.setValue(self.name + '/bin size', self.histogramSize) self.settings.setValue(self.name + '/show histograms', self.bShowHistograms) self.settings.setValue(self.name + '/marker size', self.markerSize) self.settings.setValue(self.name + '/show R2', self.bShowR2) self.plot(profile, statsResults)
def configure(self, profile, statsResults):
self.statsResults = statsResults
self.configDlg = ConfigureDialog(Ui_pValueHistogramDialog)
self.connect(self.configDlg.ui.btnXmax, QtCore.SIGNAL('clicked()'), self.setXaxisMax)
self.configDlg.ui.cboFieldToPlot.setCurrentIndex(self.configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.chkShowInset.setChecked(self.bShowInset)
self.configDlg.ui.spinInsetWidth.setValue(self.insetWidth)
self.configDlg.ui.spinInsetHeight.setValue(self.insetHeight)
self.configDlg.ui.spinInsetBinWidth.setValue(self.insetBinWidth)
self.configDlg.ui.spinXlimit.setValue(self.xLimit)
self.configDlg.ui.chkInsetLogScale.setChecked(self.insetLogScale)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.fieldToPlot = self.configDlg.ui.cboFieldToPlot.currentText()
self.bShowInset = self.configDlg.ui.chkShowInset.isChecked()
self.insetWidth = self.configDlg.ui.spinInsetWidth.value()
self.insetHeight = self.configDlg.ui.spinInsetHeight.value()
self.insetBinWidth = self.configDlg.ui.spinInsetBinWidth.value()
self.xLimit = self.configDlg.ui.spinXlimit.value()
self.insetLogScale = self.configDlg.ui.chkInsetLogScale.isChecked()
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/field to plot', self.fieldToPlot)
self.settings.setValue(self.name + '/histogram log scale', self.yAxisLogScale)
self.settings.setValue(self.name + '/histogram bin width', self.binWidth)
self.settings.setValue(self.name + '/show inset', self.bShowInset)
self.settings.setValue(self.name + '/inset width %', self.insetWidth)
self.settings.setValue(self.name + '/inset height %', self.insetHeight)
self.settings.setValue(self.name + '/inset log scale', self.insetLogScale)
self.settings.setValue(self.name + '/inset bin width', self.insetBinWidth)
self.settings.setValue(self.name + '/inset x-axis limit', self.xLimit)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
self.configDlg = ConfigureDialog(Ui_MultCompCorrectionDialog)
self.connect(self.configDlg.ui.btnXmaxFig1, QtCore.SIGNAL('clicked()'), self.setXaxisMax1)
self.connect(self.configDlg.ui.btnXmaxFig2, QtCore.SIGNAL('clicked()'), self.setXaxisMax2)
self.connect(self.configDlg.ui.btnXmaxFig3, QtCore.SIGNAL('clicked()'), self.setXaxisMax3)
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.spinXlimitFig1.setValue(self.xLimitFig1)
self.configDlg.ui.spinXlimitFig2.setValue(self.xLimitFig2)
self.configDlg.ui.spinXlimitFig3.setValue(self.xLimitFig3)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.xLimitFig1 = self.configDlg.ui.spinXlimitFig1.value()
self.xLimitFig2 = self.configDlg.ui.spinXlimitFig2.value()
self.xLimitFig3 = self.configDlg.ui.spinXlimitFig3.value()
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/histogram log scale', self.yAxisLogScale)
self.settings.setValue(self.name + '/bin width', self.binWidth)
self.settings.setValue(self.name + '/histogram x-axis limit', self.xLimitFig1)
self.settings.setValue(self.name + '/correction plot x-axis limit', self.xLimitFig2)
self.settings.setValue(self.name + '/significant features x-axis limit', self.xLimitFig3)
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.cboPercentageOrSeqCount.setEnabled(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.cboPercentageOrSeqCount.setCurrentIndex(self.configDlg.ui.cboPercentageOrSeqCount.findText(self.percentageOrSeqCount)) 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.percentageOrSeqCount = self.configDlg.ui.cboPercentageOrSeqCount.currentText() # 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(self.name + '/width', self.figWidth) self.settings.setValue(self.name + '/row height', self.figHeightPerRow) self.settings.setValue(self.name + '/field', self.sortingField) self.settings.setValue(self.name + '/sequences subplot', self.bShowBarPlot) self.settings.setValue(self.name + '/p-value labels', self.bShowPValueLabels) self.settings.setValue(self.name + '/show corrected p-values', self.bShowCorrectedPvalues) self.settings.setValue(self.name + 'use custom limits', self.bCustomLimits) self.settings.setValue(self.name + '/minimum', self.minX) self.settings.setValue(self.name + '/maximum', self.maxX) self.settings.setValue(self.name + '/marker size', self.markerSize) self.settings.setValue(self.name + '/percentage or seq count', self.percentageOrSeqCount) self.settings.setValue(self.name + '/legend position', self.legendPos) self.plot(profile, statsResults) QtGui.QApplication.instance().restoreOverrideCursor()
class ExtendedErrorBar(AbstractSamplePlotPlugin):
'''
Extended error bar plot.
'''
def __init__(self, preferences, parent=None):
AbstractSamplePlotPlugin.__init__(self, preferences, parent)
self.name = 'Extended error bar'
self.type = 'Statistical'
self.settings = preferences['Settings']
self.figWidth = self.settings.value(self.name + '/width', 7.0).toDouble()[0]
self.figHeightPerRow = self.settings.value(self.name + '/row height', 0.2).toDouble()[0]
self.sortingField = self.settings.value(self.name + '/field', 'p-values').toString()
self.bShowBarPlot = self.settings.value(self.name + '/sequences subplot', True).toBool()
self.bShowPValueLabels = self.settings.value(self.name + '/p-value labels', True).toBool()
self.bShowCorrectedPvalues = self.settings.value(self.name + '/show corrected p-values', True).toBool()
self.bCustomLimits = self.settings.value(self.name + '/use custom limits', False).toBool()
self.minX = self.settings.value(self.name + '/minimum', 0.0).toDouble()[0]
self.maxX = self.settings.value(self.name + '/maximum', 1.0).toDouble()[0]
self.markerSize = self.settings.value(self.name + '/marker size', 30).toInt()[0]
self.percentageOrSeqCount = self.settings.value(self.name + '/percentage or seq count', 'Proportion (%)').toString()
self.legendPos = self.settings.value(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.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())
profile1Colour = str(self.preferences['Sample 1 colour'].name())
profile2Colour = str(self.preferences['Sample 2 colour'].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, statsResults.confIntervMethod.bRatio)
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')
if statsResults.multCompCorrection.method != 'No correction':
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'
seqs1 = statsResults.getColumn('Seq1')
seqs2 = statsResults.getColumn('Seq2')
parentSeqs1 = statsResults.getColumn('ParentalSeq1')
parentSeqs2 = statsResults.getColumn('ParentalSeq2')
# *** Truncate feature labels
highlightedFeatures = list(self.preferences['Highlighted sample 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] + '...'
# *** Adjust effect size for axis scale
dominateInSample2 = []
percentage1 = []
percentage2 = []
for i in xrange(0, len(effectSizes)):
percentage1.append(float(seqs1[i])*100 / parentSeqs1[i])
percentage2.append(float(seqs2[i])*100 / parentSeqs2[i])
if statsResults.confIntervMethod.bRatio:
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
if self.percentageOrSeqCount == 'Proportion (%)':
# plot percentage
axNumSeq.barh(np.arange(len(features))+0.0, percentage1, height = 0.3, color=profile1Colour, zorder=10, ecolor='black')
axNumSeq.barh(np.arange(len(features))-0.3, percentage2, height = 0.3, color=profile2Colour, zorder=10, ecolor='black')
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(self.percentageOrSeqCount)
maxPercentage = max(max(percentage1), max(percentage2))
axNumSeq.set_xticks([0, maxPercentage])
axNumSeq.set_xlim([0, maxPercentage*1.05])
maxPercentageStr = '%.1f' % maxPercentage
axNumSeq.set_xticklabels(['0.0', maxPercentageStr])
else:
# plot sequence count
axNumSeq.barh(np.arange(len(features))+0.0, seqs1, height = 0.3, color=profile1Colour, zorder=10, ecolor='black')
axNumSeq.barh(np.arange(len(features))-0.3, seqs2, height = 0.3, color=profile2Colour, zorder=10, ecolor='black')
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(self.percentageOrSeqCount)
maxSeqs = max(max(seqs1), max(seqs2))
axNumSeq.set_xticks([0, maxSeqs])
axNumSeq.set_xlim([0, maxSeqs*1.05])
axNumSeq.set_xticklabels([0, str(maxSeqs)])
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=profile1Colour, mec='black', ecolor='black', zorder=10)
effectSizesSample2 = [effectSizes[value] for value in dominateInSample2]
axErrorbar.plot(effectSizesSample2, dominateInSample2, ls='', marker='o', ms=markerSize, mfc=profile2Colour, mec='black', zorder=100)
if statsResults.confIntervMethod.bRatio:
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(statsResults.confIntervMethod.plotLabel)
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 highlightedFeatures:
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
for loc, spine in axRight.spines.iteritems():
spine.set_color('none')
# *** Legend
# *** Legend
if self.legendPos != -1:
legend1 = Rectangle((0, 0), 1, 1, fc=profile1Colour)
legend2 = Rectangle((0, 0), 1, 1, fc=profile2Colour)
legend = self.fig.legend([legend1, legend2], (statsResults.profile.sampleNames[0], statsResults.profile.sampleNames[1]), 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.cboPercentageOrSeqCount.setEnabled(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.cboPercentageOrSeqCount.setCurrentIndex(self.configDlg.ui.cboPercentageOrSeqCount.findText(self.percentageOrSeqCount))
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.percentageOrSeqCount = self.configDlg.ui.cboPercentageOrSeqCount.currentText()
# 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(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/row height', self.figHeightPerRow)
self.settings.setValue(self.name + '/field', self.sortingField)
self.settings.setValue(self.name + '/sequences subplot', self.bShowBarPlot)
self.settings.setValue(self.name + '/p-value labels', self.bShowPValueLabels)
self.settings.setValue(self.name + '/show corrected p-values', self.bShowCorrectedPvalues)
self.settings.setValue(self.name + 'use custom limits', self.bCustomLimits)
self.settings.setValue(self.name + '/minimum', self.minX)
self.settings.setValue(self.name + '/maximum', self.maxX)
self.settings.setValue(self.name + '/marker size', self.markerSize)
self.settings.setValue(self.name + '/percentage or seq count', self.percentageOrSeqCount)
self.settings.setValue(self.name + '/legend position', self.legendPos)
self.plot(profile, statsResults)
QtGui.QApplication.instance().restoreOverrideCursor()
class pValueHistogram(AbstractSamplePlotPlugin):
'''
p-value histogram plot.
'''
def __init__(self, preferences, parent=None):
AbstractSamplePlotPlugin.__init__(self, preferences, parent)
self.preferences = preferences
self.name = 'p-value histogram'
self.type = 'Statistical'
self.settings = preferences['Settings']
self.figWidth = self.settings.value(self.name + '/width', 7.0).toDouble()[0]
self.figHeight = self.settings.value(self.name + '/height', 7.0).toDouble()[0]
self.fieldToPlot = self.settings.value(self.name + '/field to plot', 'p-values (corrected)').toString()
self.yAxisLogScale = self.settings.value(self.name + '/histogram log scale', False).toBool()
self.binWidth = self.settings.value(self.name + '/histogram bin width', 0.01).toDouble()[0]
self.bShowInset = self.settings.value(self.name + '/show inset', True).toBool()
self.insetWidth = self.settings.value(self.name + '/inset width %', 60.0).toDouble()[0]
self.insetHeight = self.settings.value(self.name + '/inset height %', 60.0).toDouble()[0]
self.insetLogScale = self.settings.value(self.name + '/inset log scale', False).toBool()
self.insetBinWidth = self.settings.value(self.name + '/inset bin width', 0.002).toDouble()[0]
self.xLimit = self.settings.value(self.name + '/inset x-axis limit', 0.05).toDouble()[0]
def mirrorProperties(self, plotToCopy):
self.name = plotToCopy.name
self.figWidth = plotToCopy.figWidth
self.figHeight = plotToCopy.figHeight
self.yAxisLogScale = plotToCopy.yAxisLogScale
self.fieldToPlot = plotToCopy.fieldToPlot
self.bShowInset = plotToCopy.bShowInset
self.insetWidth = plotToCopy.insetWidth
self.insetHeight = plotToCopy.insetHeight
self.insetBinWidth = plotToCopy.insetBinWidth
self.xLimit = plotToCopy.xLimit
self.insetLogScale = plotToCopy.insetLogScale
def plot(self, profile, statsResults):
if len(statsResults.activeData) <= 0:
self.emptyAxis()
return
axesColour = str(self.preferences['Axes colour'].name())
# *** Get data to plot
if self.fieldToPlot == 'p-values':
data = statsResults.getColumn('pValues')
xLabel = 'p-value'
elif self.fieldToPlot == 'p-values (corrected)':
data = statsResults.getColumn('pValuesCorrected')
xLabel = 'p-value (corrected)'
# *** Set size of figure
self.fig.clear()
self.fig.set_size_inches(self.figWidth, self.figHeight)
heightBottomLabels = 0.4 # inches
widthSideLabel = 0.5 # inches
padding = 0.2 # inches
axesHist = self.fig.add_axes([widthSideLabel/self.figWidth,heightBottomLabels/self.figHeight,\
1.0-(widthSideLabel+padding)/self.figWidth,\
1.0-(heightBottomLabels+padding)/self.figHeight])
# *** Histogram plot
bins = [0.0]
binWidth = self.binWidth
binEnd = binWidth
while binEnd <= 1.0:
bins.append(binEnd)
binEnd += binWidth
n, bins, patch = axesHist.hist(data, bins=bins, log=self.yAxisLogScale,color=(0.5,0.5,0.5))
axesHist.set_xlabel(xLabel)
axesHist.set_ylabel('Number of features')
# *** Prettify plot
for a in axesHist.yaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for a in axesHist.xaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for line in axesHist.yaxis.get_ticklines():
line.set_color(axesColour)
for line in axesHist.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in axesHist.spines.iteritems():
if loc in ['right','top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
# *** Plot inset
if self.bShowInset:
bins = [0.0]
binWidth = self.insetBinWidth
binEnd = binWidth
while binEnd <= self.xLimit:
bins.append(binEnd)
binEnd += binWidth
widthStr = str(self.insetWidth) + '%'
heightStr = str(self.insetHeight) + '%'
axins = inset_axes(axesHist, width=widthStr, height=heightStr, loc=1)
filteredData = [d for d in data if d <= self.xLimit]
if filteredData:
n, bins, patch = axins.hist(filteredData, bins=bins, log=self.insetLogScale, color=(0.5,0.5,0.5))
axins.set_xlim(0, self.xLimit)
# *** Prettify inset
for a in axins.yaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for a in axins.xaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for line in axins.yaxis.get_ticklines():
line.set_color(axesColour)
for line in axins.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in axins.spines.iteritems():
if loc in ['right','top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
self.updateGeometry()
self.draw()
def configure(self, profile, statsResults):
self.statsResults = statsResults
self.configDlg = ConfigureDialog(Ui_pValueHistogramDialog)
self.connect(self.configDlg.ui.btnXmax, QtCore.SIGNAL('clicked()'), self.setXaxisMax)
self.configDlg.ui.cboFieldToPlot.setCurrentIndex(self.configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.chkShowInset.setChecked(self.bShowInset)
self.configDlg.ui.spinInsetWidth.setValue(self.insetWidth)
self.configDlg.ui.spinInsetHeight.setValue(self.insetHeight)
self.configDlg.ui.spinInsetBinWidth.setValue(self.insetBinWidth)
self.configDlg.ui.spinXlimit.setValue(self.xLimit)
self.configDlg.ui.chkInsetLogScale.setChecked(self.insetLogScale)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.fieldToPlot = self.configDlg.ui.cboFieldToPlot.currentText()
self.bShowInset = self.configDlg.ui.chkShowInset.isChecked()
self.insetWidth = self.configDlg.ui.spinInsetWidth.value()
self.insetHeight = self.configDlg.ui.spinInsetHeight.value()
self.insetBinWidth = self.configDlg.ui.spinInsetBinWidth.value()
self.xLimit = self.configDlg.ui.spinXlimit.value()
self.insetLogScale = self.configDlg.ui.chkInsetLogScale.isChecked()
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/field to plot', self.fieldToPlot)
self.settings.setValue(self.name + '/histogram log scale', self.yAxisLogScale)
self.settings.setValue(self.name + '/histogram bin width', self.binWidth)
self.settings.setValue(self.name + '/show inset', self.bShowInset)
self.settings.setValue(self.name + '/inset width %', self.insetWidth)
self.settings.setValue(self.name + '/inset height %', self.insetHeight)
self.settings.setValue(self.name + '/inset log scale', self.insetLogScale)
self.settings.setValue(self.name + '/inset bin width', self.insetBinWidth)
self.settings.setValue(self.name + '/inset x-axis limit', self.xLimit)
self.plot(profile, statsResults)
def setXaxisMax(self):
# *** Get data to plot
if self.configDlg.ui.cboFieldToPlot.currentText() == 'p-values':
data = self.statsResults.getColumn('pValues')
else:
data = self.statsResults.getColumn('pValuesCorrected')
self.configDlg.ui.spinXlimit.setValue(max(data))
class MultCompCorrectionPlots(AbstractSamplePlotPlugin):
'''
Sequence histogram plot.
'''
def __init__(self, preferences, parent=None):
AbstractSamplePlotPlugin.__init__(self, preferences, parent)
self.preferences = preferences
self.name = 'Multiple comparison plots'
self.type = 'Statistical'
self.settings = preferences['Settings']
self.figWidth = self.settings.value(self.name + '/width',
7.0).toDouble()[0]
self.figHeight = self.settings.value(self.name + '/height',
3.5).toDouble()[0]
self.yAxisLogScale = self.settings.value(
self.name + '/histogram log scale', False).toBool()
self.binWidth = self.settings.value(self.name + '/bin width',
0.01).toDouble()[0]
self.xLimitFig1 = self.settings.value(
self.name + '/histogram x-axis limit', 0.1).toDouble()[0]
self.xLimitFig2 = self.settings.value(
self.name + '/correction plot x-axis limit', 1.0).toDouble()[0]
self.xLimitFig3 = self.settings.value(
self.name + '/significant features x-axis limit',
0.1).toDouble()[0]
self.xMax = 0
def mirrorProperties(self, plotToCopy):
self.name = plotToCopy.name
self.figWidth = plotToCopy.figWidth
self.figHeight = plotToCopy.figHeight
self.yAxisLogScale = plotToCopy.yAxisLogScale
self.binWidth = plotToCopy.binWidth
self.xLimitFig1 = plotToCopy.xLimitFig1
self.xLimitFig2 = plotToCopy.xLimitFig2
self.xLimitFig3 = plotToCopy.xLimitFig3
self.xMax = plotToCopy.xMax
def plot(self, profile, statsResults):
if len(statsResults.activeData) <= 0:
self.emptyAxis()
return
axesColour = str(self.preferences['Axes colour'].name())
# *** Get p-values and effect size
rawValues = statsResults.getColumn('pValues')
correctedValues = statsResults.getColumn('pValuesCorrected')
# *** Get labels
if statsResults.multCompCorrection.method == 'False discovery rate':
xLabel = 'q-value'
yLabel = 'p-value'
else:
xLabel = 'corrected p-value'
yLabel = 'raw p-value'
# *** Set size of figure
self.fig.clear()
self.fig.set_size_inches(self.figWidth, self.figHeight)
self.fig.subplots_adjust(wspace=0.4)
self.fig.subplots_adjust(bottom=0.15)
self.fig.subplots_adjust(top=0.95)
self.fig.subplots_adjust(left=0.07)
self.fig.subplots_adjust(right=0.97)
# Sort p-values
pValues = zip(correctedValues, rawValues)
pValues.sort()
correctedValues = [pValue[0] for pValue in pValues]
rawValues = [pValue[1] for pValue in pValues]
self.xMax = max(correctedValues)
# Plot effect size vs. corrected p-value
ax1 = self.fig.add_subplot(1, 3, 1)
bins = [0.0]
binWidth = self.binWidth
binEnd = binWidth
while binEnd <= self.xLimitFig1:
bins.append(binEnd)
binEnd += binWidth
x = [value for value in correctedValues if value <= self.xLimitFig1]
if x:
n, bins, patch = ax1.hist(x,
bins=bins,
log=self.yAxisLogScale,
color=(0.5, 0.5, 0.5))
ax1.set_xlabel(xLabel)
ax1.set_ylabel('Number of features')
ax1.set_xlim(0, self.xLimitFig1)
for label in ax1.get_xticklabels():
label.set_rotation(90)
for a in ax1.yaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for a in ax1.xaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for line in ax1.yaxis.get_ticklines():
line.set_color(axesColour)
for line in ax1.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in ax1.spines.iteritems():
if loc in ['right', 'top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
# Plot corrected p-values vs raw p-values
ax2 = self.fig.add_subplot(1, 3, 2)
x = [value for value in correctedValues if value <= self.xLimitFig2]
y = rawValues[0:len(x)]
ax2.plot(x, y, 'o', markersize=4, mfc=(0.5, 0.5, 0.5))
ax2.set_xlabel(xLabel)
ax2.set_ylabel(yLabel)
ax2.set_xlim(0, self.xLimitFig2)
for label in ax2.get_xticklabels():
label.set_rotation(90)
for a in ax2.yaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for a in ax2.xaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for line in ax2.yaxis.get_ticklines():
line.set_color(axesColour)
for line in ax2.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in ax2.spines.iteritems():
if loc in ['right', 'top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
# Plot corrected p-values vs. number of significant features
ax3 = self.fig.add_subplot(1, 3, 3)
x = [value for value in correctedValues if value <= self.xLimitFig3]
x = correctedValues[
0:len(x) +
1] # add in one extra point so the plot fills the entire x-axis
ax3.plot(x, np.arange(len(x)), 'k-')
ax3.set_xlabel(xLabel)
ax3.set_ylabel('# significant features')
ax3.set_xlim(0, self.xLimitFig3)
for label in ax3.get_xticklabels():
label.set_rotation(90)
for a in ax3.yaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for a in ax3.xaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for line in ax3.yaxis.get_ticklines():
line.set_color(axesColour)
for line in ax3.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in ax3.spines.iteritems():
if loc in ['right', 'top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
self.updateGeometry()
self.draw()
def configure(self, profile, statsResults):
self.configDlg = ConfigureDialog(Ui_MultCompCorrectionDialog)
self.connect(self.configDlg.ui.btnXmaxFig1, QtCore.SIGNAL('clicked()'),
self.setXaxisMax1)
self.connect(self.configDlg.ui.btnXmaxFig2, QtCore.SIGNAL('clicked()'),
self.setXaxisMax2)
self.connect(self.configDlg.ui.btnXmaxFig3, QtCore.SIGNAL('clicked()'),
self.setXaxisMax3)
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.spinXlimitFig1.setValue(self.xLimitFig1)
self.configDlg.ui.spinXlimitFig2.setValue(self.xLimitFig2)
self.configDlg.ui.spinXlimitFig3.setValue(self.xLimitFig3)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.xLimitFig1 = self.configDlg.ui.spinXlimitFig1.value()
self.xLimitFig2 = self.configDlg.ui.spinXlimitFig2.value()
self.xLimitFig3 = self.configDlg.ui.spinXlimitFig3.value()
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/histogram log scale',
self.yAxisLogScale)
self.settings.setValue(self.name + '/bin width', self.binWidth)
self.settings.setValue(self.name + '/histogram x-axis limit',
self.xLimitFig1)
self.settings.setValue(self.name + '/correction plot x-axis limit',
self.xLimitFig2)
self.settings.setValue(
self.name + '/significant features x-axis limit',
self.xLimitFig3)
self.plot(profile, statsResults)
def setXaxisMax1(self):
self.configDlg.ui.spinXlimitFig1.setValue(self.xMax)
def setXaxisMax2(self):
self.configDlg.ui.spinXlimitFig2.setValue(self.xMax)
def setXaxisMax3(self):
self.configDlg.ui.spinXlimitFig3.setValue(self.xMax)
class SeqHistogram(AbstractSamplePlotPlugin):
'''
Sequence histogram plot.
'''
def __init__(self, preferences, parent=None):
AbstractSamplePlotPlugin.__init__(self, preferences, parent)
self.preferences = preferences
self.name = 'Sequence histogram'
self.type = 'Exploratory'
self.settings = preferences['Settings']
self.figWidth = self.settings.value(self.name + '/width', 7.0).toDouble()[0]
self.figHeight = self.settings.value(self.name + '/height', 7.0).toDouble()[0]
self.bCustomBinWidth = self.settings.value(self.name + '/custom bin width', False).toBool()
self.binWidth = self.settings.value(self.name + '/bin width', 100.0).toDouble()[0]
self.yAxisLogScale = self.settings.value(self.name + '/log scale', False).toBool()
self.bCustomXaxis = self.settings.value(self.name + '/custom x-axis extents', False).toBool()
self.xLimitLeft = self.settings.value(self.name + '/min value', 0.0).toDouble()[0]
self.xLimitRight = self.settings.value(self.name + '/max value', 1.0).toDouble()[0]
self.legendPos = self.settings.value(self.name + '/legend position', 0).toInt()[0]
def mirrorProperties(self, plotToCopy):
self.name = plotToCopy.name
self.figWidth = plotToCopy.figWidth
self.figHeight = plotToCopy.figHeight
self.bCustomBinWidth = plotToCopy.bCustomBinWidth
self.binWidth = plotToCopy.binWidth
self.yAxisLogScale = plotToCopy.yAxisLogScale
self.bCustomXaxis = plotToCopy.bCustomXaxis
self.xLimitLeft = plotToCopy.xLimitLeft
self.xLimitRight = plotToCopy.xLimitRight
self.legendPos = plotToCopy.legendPos
def plot(self, profile, statsResults):
if len(profile.profileDict) <= 0:
self.emptyAxis()
return
# *** Colour of plot elements
axesColour = str(self.preferences['Axes colour'].name())
profile1Colour = str(self.preferences['Sample 1 colour'].name())
profile2Colour = str(self.preferences['Sample 2 colour'].name())
# *** Get sequence counts
seqs1 = profile.getSequenceCounts(0)
seqs2 = profile.getSequenceCounts(1)
# *** Set x-axis limit
self.xMin = min(min(seqs1),min(seqs2))
if self.xLimitLeft == None:
self.xLimitLeft = self.xMin
self.xMax = max(max(seqs1),max(seqs2))
if self.xLimitRight == None:
self.xLimitRight = self.xMax
# Set bin width
if not self.bCustomBinWidth:
self.binWidth = (self.xMax - self.xMin) / 40
# *** Set size of figure
self.fig.clear()
self.fig.set_size_inches(self.figWidth, self.figHeight)
heightBottomLabels = 0.4 # inches
widthSideLabel = 0.5 # inches
padding = 0.2 # inches
axesHist = self.fig.add_axes([widthSideLabel/self.figWidth,heightBottomLabels/self.figHeight,\
1.0-(widthSideLabel+padding)/self.figWidth,\
1.0-(heightBottomLabels+padding)/self.figHeight])
# *** Histogram plot
bins = [0]
binEnd = self.binWidth
while binEnd <= self.xMax:
bins.append(binEnd)
binEnd += self.binWidth
bins.append(binEnd)
n, b, patches = axesHist.hist([seqs1, seqs2], bins=bins, log=self.yAxisLogScale)
for patch in patches[0]:
patch.set_facecolor(profile1Colour)
for patch in patches[1]:
patch.set_facecolor(profile2Colour)
if self.bCustomXaxis:
axesHist.set_xlim(self.xLimitLeft, self.xLimitRight)
axesHist.set_xlabel('Sequences')
axesHist.set_ylabel('Number of features')
# *** Prettify plot
if self.legendPos != -1:
legend = axesHist.legend([patches[0][0], patches[1][0]], (profile.sampleNames[0], profile.sampleNames[1]), loc=self.legendPos)
legend.get_frame().set_linewidth(0)
for a in axesHist.yaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for a in axesHist.xaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for line in axesHist.yaxis.get_ticklines():
line.set_color(axesColour)
for line in axesHist.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in axesHist.spines.iteritems():
if loc in ['right','top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
self.updateGeometry()
self.draw()
def configure(self, profile, statsResults):
self.profile = profile
self.configDlg = ConfigureDialog(Ui_SeqHistogramDialog)
self.connect(self.configDlg.ui.chkCustomBinWidth, QtCore.SIGNAL('toggled(bool)'), self.changeCustomBinWidth)
self.connect(self.configDlg.ui.chkCustomXaxis, QtCore.SIGNAL('toggled(bool)'), self.changeCustomXaxis)
self.connect(self.configDlg.ui.btnXmin, QtCore.SIGNAL('clicked()'), self.setXaxisMin)
self.connect(self.configDlg.ui.btnXmax, QtCore.SIGNAL('clicked()'), self.setXaxisMax)
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.chkCustomBinWidth.setChecked(self.bCustomBinWidth)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.chkCustomXaxis.setChecked(self.bCustomXaxis)
self.configDlg.ui.spinXmin.setValue(self.xLimitLeft)
self.configDlg.ui.spinXmax.setValue(self.xLimitRight)
self.changeCustomBinWidth()
self.changeCustomXaxis()
# legend position
if self.legendPos == 0:
self.configDlg.ui.radioLegendPosBest.setDown(True)
elif self.legendPos == 1:
self.configDlg.ui.radioLegendPosUpperRight.setChecked(True)
elif self.legendPos == 7:
self.configDlg.ui.radioLegendPosCentreRight.setChecked(True)
elif self.legendPos == 4:
self.configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 2:
self.configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 6:
self.configDlg.ui.radioLegendPosCentreLeft.setChecked(True)
elif self.legendPos == 3:
self.configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
else:
self.configDlg.ui.radioLegendPosNone.setChecked(True)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.bCustomBinWidth = self.configDlg.ui.chkCustomBinWidth.isChecked()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.bCustomXaxis = self.configDlg.ui.chkCustomXaxis.isChecked()
self.xLimitLeft = self.configDlg.ui.spinXmin.value()
self.xLimitRight = self.configDlg.ui.spinXmax.value()
# legend position
if self.configDlg.ui.radioLegendPosBest.isChecked() == True:
self.legendPos = 0
elif self.configDlg.ui.radioLegendPosUpperRight.isChecked() == True:
self.legendPos = 1
elif self.configDlg.ui.radioLegendPosCentreRight.isChecked() == True:
self.legendPos = 7
elif self.configDlg.ui.radioLegendPosLowerRight.isChecked() == True:
self.legendPos = 4
elif self.configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif self.configDlg.ui.radioLegendPosCentreLeft.isChecked() == True:
self.legendPos = 6
elif self.configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
else:
self.legendPos = -1
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/custom bin width', self.bCustomBinWidth)
self.settings.setValue(self.name + '/bin width', self.binWidth)
self.settings.setValue(self.name + '/log scale', self.yAxisLogScale)
self.settings.setValue(self.name + '/custom x-axis extents', self.bCustomXaxis)
self.settings.setValue(self.name + '/min value', self.xLimitLeft)
self.settings.setValue(self.name + '/max value', self.xLimitRight)
self.settings.setValue(self.name + '/legend position', self.legendPos)
self.plot(profile, statsResults)
def changeCustomBinWidth(self):
self.configDlg.ui.spinBinWidth.setEnabled(self.configDlg.ui.chkCustomBinWidth.isChecked())
def changeCustomXaxis(self):
self.configDlg.ui.spinXmin.setEnabled(self.configDlg.ui.chkCustomXaxis.isChecked())
self.configDlg.ui.spinXmax.setEnabled(self.configDlg.ui.chkCustomXaxis.isChecked())
def setXaxisMin(self):
seqs1 = self.profile.getSequenceCounts(0)
seqs2 = self.profile.getSequenceCounts(1)
self.configDlg.ui.spinXmin.setValue(min(min(seqs1), min(seqs2)))
def setXaxisMax(self):
seqs1 = self.profile.getSequenceCounts(0)
seqs2 = self.profile.getSequenceCounts(1)
self.configDlg.ui.spinXmax.setValue(max(max(seqs1), max(seqs2)))
def configure(self, profile, statsResults):
configDlg = ConfigureDialog(Ui_ProfileBarPlotDialog)
# set enabled state of widgets
configDlg.ui.spinEndCapSize.setEnabled(self.bShowCIs)
configDlg.ui.spinPvalueThreshold.setEnabled(self.bShowPvalue)
# set current values
configDlg.ui.cboFieldToPlot.setCurrentIndex(
configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
configDlg.ui.spinFigColWidth.setValue(self.figColWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.chkShowCIs.setChecked(self.bShowCIs)
configDlg.ui.spinEndCapSize.setValue(self.endCapSize)
configDlg.ui.spinFeaturesToShow.setValue(self.numFeaturesToShow)
configDlg.ui.chkOnlyActiveFeatures.setChecked(self.bOnlyActiveFeatures)
# 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.spinBarWidth.setValue(self.barWidth)
configDlg.ui.chkShowPvalue.setChecked(self.bShowPvalue)
configDlg.ui.spinPvalueThreshold.setValue(self.pValueThreshold)
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.bShowCIs = configDlg.ui.chkShowCIs.isChecked()
self.endCapSize = configDlg.ui.spinEndCapSize.value()
self.numFeaturesToShow = configDlg.ui.spinFeaturesToShow.value()
self.bOnlyActiveFeatures = configDlg.ui.chkOnlyActiveFeatures.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.barWidth = configDlg.ui.spinBarWidth.value()
self.bShowPvalue = configDlg.ui.chkShowPvalue.isChecked()
self.pValueThreshold = configDlg.ui.spinPvalueThreshold.value()
self.settings.setValue(self.name + '/column width',
self.figColWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/field to plot',
self.fieldToPlot)
self.settings.setValue(self.name + '/legend position',
self.legendPos)
self.settings.setValue(self.name + '/show cis', self.bShowCIs)
self.settings.setValue(self.name + '/end cap size',
self.endCapSize)
self.settings.setValue(self.name + '/features to show',
self.numFeaturesToShow)
self.settings.setValue(self.name + '/bar width (%)', self.barWidth)
self.settings.setValue(self.name + '/show p-value',
self.bShowPvalue)
self.settings.setValue(self.name + '/p-value threshold',
self.pValueThreshold)
self.settings.setValue(self.name + '/only active features',
self.bOnlyActiveFeatures)
self.plot(profile, statsResults)
class MultCompCorrectionPlots(AbstractSamplePlotPlugin):
'''
Sequence histogram plot.
'''
def __init__(self, preferences, parent=None):
AbstractSamplePlotPlugin.__init__(self, preferences, parent)
self.preferences = preferences
self.name = 'Multiple comparison plots'
self.type = 'Statistical'
self.settings = preferences['Settings']
self.figWidth = self.settings.value(self.name + '/width', 7.0).toDouble()[0]
self.figHeight = self.settings.value(self.name + '/height', 3.5).toDouble()[0]
self.yAxisLogScale = self.settings.value(self.name + '/histogram log scale', False).toBool()
self.binWidth = self.settings.value(self.name + '/bin width', 0.01).toDouble()[0]
self.xLimitFig1 = self.settings.value(self.name + '/histogram x-axis limit', 0.1).toDouble()[0]
self.xLimitFig2 = self.settings.value(self.name + '/correction plot x-axis limit', 1.0).toDouble()[0]
self.xLimitFig3 = self.settings.value(self.name + '/significant features x-axis limit', 0.1).toDouble()[0]
self.xMax = 0
def mirrorProperties(self, plotToCopy):
self.name = plotToCopy.name
self.figWidth = plotToCopy.figWidth
self.figHeight = plotToCopy.figHeight
self.yAxisLogScale = plotToCopy.yAxisLogScale
self.binWidth = plotToCopy.binWidth
self.xLimitFig1 = plotToCopy.xLimitFig1
self.xLimitFig2 = plotToCopy.xLimitFig2
self.xLimitFig3 = plotToCopy.xLimitFig3
self.xMax = plotToCopy.xMax
def plot(self, profile, statsResults):
if len(statsResults.activeData) <= 0:
self.emptyAxis()
return
axesColour = str(self.preferences['Axes colour'].name())
# *** Get p-values and effect size
rawValues = statsResults.getColumn('pValues')
correctedValues = statsResults.getColumn('pValuesCorrected')
# *** Get labels
if statsResults.multCompCorrection.method == 'False discovery rate':
xLabel = 'q-value'
yLabel = 'p-value'
else:
xLabel = 'corrected p-value'
yLabel = 'raw p-value'
# *** Set size of figure
self.fig.clear()
self.fig.set_size_inches(self.figWidth, self.figHeight)
self.fig.subplots_adjust(wspace = 0.4)
self.fig.subplots_adjust(bottom = 0.15)
self.fig.subplots_adjust(top = 0.95)
self.fig.subplots_adjust(left = 0.07)
self.fig.subplots_adjust(right = 0.97)
# Sort p-values
pValues = zip(correctedValues, rawValues)
pValues.sort()
correctedValues = [pValue[0] for pValue in pValues]
rawValues = [pValue[1] for pValue in pValues]
self.xMax = max(correctedValues)
# Plot effect size vs. corrected p-value
ax1 = self.fig.add_subplot(1,3,1)
bins = [0.0]
binWidth = self.binWidth
binEnd = binWidth
while binEnd <= self.xLimitFig1:
bins.append(binEnd)
binEnd += binWidth
x = [value for value in correctedValues if value <= self.xLimitFig1]
if x:
n, bins, patch = ax1.hist(x, bins=bins, log=self.yAxisLogScale, color=(0.5,0.5,0.5))
ax1.set_xlabel(xLabel)
ax1.set_ylabel('Number of features')
ax1.set_xlim(0, self.xLimitFig1)
for label in ax1.get_xticklabels():
label.set_rotation(90)
for a in ax1.yaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for a in ax1.xaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for line in ax1.yaxis.get_ticklines():
line.set_color(axesColour)
for line in ax1.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in ax1.spines.iteritems():
if loc in ['right','top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
# Plot corrected p-values vs raw p-values
ax2 = self.fig.add_subplot(1,3,2)
x = [value for value in correctedValues if value <= self.xLimitFig2]
y = rawValues[0:len(x)]
ax2.plot(x,y,'o', markersize=4, mfc=(0.5,0.5,0.5))
ax2.set_xlabel(xLabel)
ax2.set_ylabel(yLabel)
ax2.set_xlim(0, self.xLimitFig2)
for label in ax2.get_xticklabels():
label.set_rotation(90)
for a in ax2.yaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for a in ax2.xaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for line in ax2.yaxis.get_ticklines():
line.set_color(axesColour)
for line in ax2.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in ax2.spines.iteritems():
if loc in ['right','top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
# Plot corrected p-values vs. number of significant features
ax3 = self.fig.add_subplot(1,3,3)
x = [value for value in correctedValues if value <= self.xLimitFig3]
x = correctedValues[0:len(x)+1] # add in one extra point so the plot fills the entire x-axis
ax3.plot(x, np.arange(len(x)),'k-')
ax3.set_xlabel(xLabel)
ax3.set_ylabel('# significant features')
ax3.set_xlim(0, self.xLimitFig3)
for label in ax3.get_xticklabels():
label.set_rotation(90)
for a in ax3.yaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for a in ax3.xaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for line in ax3.yaxis.get_ticklines():
line.set_color(axesColour)
for line in ax3.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in ax3.spines.iteritems():
if loc in ['right','top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
self.updateGeometry()
self.draw()
def configure(self, profile, statsResults):
self.configDlg = ConfigureDialog(Ui_MultCompCorrectionDialog)
self.connect(self.configDlg.ui.btnXmaxFig1, QtCore.SIGNAL('clicked()'), self.setXaxisMax1)
self.connect(self.configDlg.ui.btnXmaxFig2, QtCore.SIGNAL('clicked()'), self.setXaxisMax2)
self.connect(self.configDlg.ui.btnXmaxFig3, QtCore.SIGNAL('clicked()'), self.setXaxisMax3)
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.spinXlimitFig1.setValue(self.xLimitFig1)
self.configDlg.ui.spinXlimitFig2.setValue(self.xLimitFig2)
self.configDlg.ui.spinXlimitFig3.setValue(self.xLimitFig3)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.xLimitFig1 = self.configDlg.ui.spinXlimitFig1.value()
self.xLimitFig2 = self.configDlg.ui.spinXlimitFig2.value()
self.xLimitFig3 = self.configDlg.ui.spinXlimitFig3.value()
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/histogram log scale', self.yAxisLogScale)
self.settings.setValue(self.name + '/bin width', self.binWidth)
self.settings.setValue(self.name + '/histogram x-axis limit', self.xLimitFig1)
self.settings.setValue(self.name + '/correction plot x-axis limit', self.xLimitFig2)
self.settings.setValue(self.name + '/significant features x-axis limit', self.xLimitFig3)
self.plot(profile, statsResults)
def setXaxisMax1(self):
self.configDlg.ui.spinXlimitFig1.setValue(self.xMax)
def setXaxisMax2(self):
self.configDlg.ui.spinXlimitFig2.setValue(self.xMax)
def setXaxisMax3(self):
self.configDlg.ui.spinXlimitFig3.setValue(self.xMax)
def configure(self, profile, statsResults): configDlg = ConfigureDialog(Ui_ProfileBarPlotDialog) # set enabled state of widgets configDlg.ui.spinEndCapSize.setEnabled(self.bShowCIs) configDlg.ui.spinPvalueThreshold.setEnabled(self.bShowPvalue) # set current values configDlg.ui.cboFieldToPlot.setCurrentIndex(configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot)) configDlg.ui.spinFigColWidth.setValue(self.figColWidth) configDlg.ui.spinFigHeight.setValue(self.figHeight) configDlg.ui.chkShowCIs.setChecked(self.bShowCIs) configDlg.ui.spinEndCapSize.setValue(self.endCapSize) configDlg.ui.spinFeaturesToShow.setValue(self.numFeaturesToShow) configDlg.ui.chkOnlyActiveFeatures.setChecked(self.bOnlyActiveFeatures) # 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.spinBarWidth.setValue(self.barWidth) configDlg.ui.chkShowPvalue.setChecked(self.bShowPvalue) configDlg.ui.spinPvalueThreshold.setValue(self.pValueThreshold) 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.bShowCIs = configDlg.ui.chkShowCIs.isChecked() self.endCapSize = configDlg.ui.spinEndCapSize.value() self.numFeaturesToShow = configDlg.ui.spinFeaturesToShow.value() self.bOnlyActiveFeatures = configDlg.ui.chkOnlyActiveFeatures.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.barWidth = configDlg.ui.spinBarWidth.value() self.bShowPvalue = configDlg.ui.chkShowPvalue.isChecked() self.pValueThreshold = configDlg.ui.spinPvalueThreshold.value() self.settings.setValue(self.name + '/column width', self.figColWidth) self.settings.setValue(self.name + '/height', self.figHeight) self.settings.setValue(self.name + '/field to plot', self.fieldToPlot) self.settings.setValue(self.name + '/legend position', self.legendPos) self.settings.setValue(self.name + '/show cis', self.bShowCIs) self.settings.setValue(self.name + '/end cap size', self.endCapSize) self.settings.setValue(self.name + '/features to show', self.numFeaturesToShow) self.settings.setValue(self.name + '/bar width (%)', self.barWidth) self.settings.setValue(self.name + '/show p-value', self.bShowPvalue) self.settings.setValue(self.name + '/p-value threshold', self.pValueThreshold) self.settings.setValue(self.name + '/only active features', self.bOnlyActiveFeatures) 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.cboPercentageOrSeqCount.setEnabled(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.cboPercentageOrSeqCount.setCurrentIndex(
self.configDlg.ui.cboPercentageOrSeqCount.findText(
self.percentageOrSeqCount))
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.percentageOrSeqCount = self.configDlg.ui.cboPercentageOrSeqCount.currentText(
)
# 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(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/row height',
self.figHeightPerRow)
self.settings.setValue(self.name + '/field', self.sortingField)
self.settings.setValue(self.name + '/sequences subplot',
self.bShowBarPlot)
self.settings.setValue(self.name + '/p-value labels',
self.bShowPValueLabels)
self.settings.setValue(self.name + '/show corrected p-values',
self.bShowCorrectedPvalues)
self.settings.setValue(self.name + 'use custom limits',
self.bCustomLimits)
self.settings.setValue(self.name + '/minimum', self.minX)
self.settings.setValue(self.name + '/maximum', self.maxX)
self.settings.setValue(self.name + '/marker size', self.markerSize)
self.settings.setValue(self.name + '/percentage or seq count',
self.percentageOrSeqCount)
self.settings.setValue(self.name + '/legend position',
self.legendPos)
self.plot(profile, statsResults)
QtGui.QApplication.instance().restoreOverrideCursor()
class ExtendedErrorBar(AbstractSamplePlotPlugin):
'''
Extended error bar plot.
'''
def __init__(self, preferences, parent=None):
AbstractSamplePlotPlugin.__init__(self, preferences, parent)
self.name = 'Extended error bar'
self.type = 'Statistical'
self.settings = preferences['Settings']
self.figWidth = self.settings.value(self.name + '/width',
7.0).toDouble()[0]
self.figHeightPerRow = self.settings.value(self.name + '/row height',
0.2).toDouble()[0]
self.sortingField = self.settings.value(self.name + '/field',
'p-values').toString()
self.bShowBarPlot = self.settings.value(
self.name + '/sequences subplot', True).toBool()
self.bShowPValueLabels = self.settings.value(
self.name + '/p-value labels', True).toBool()
self.bShowCorrectedPvalues = self.settings.value(
self.name + '/show corrected p-values', True).toBool()
self.bCustomLimits = self.settings.value(
self.name + '/use custom limits', False).toBool()
self.minX = self.settings.value(self.name + '/minimum',
0.0).toDouble()[0]
self.maxX = self.settings.value(self.name + '/maximum',
1.0).toDouble()[0]
self.markerSize = self.settings.value(self.name + '/marker size',
30).toInt()[0]
self.percentageOrSeqCount = self.settings.value(
self.name + '/percentage or seq count',
'Proportion (%)').toString()
self.legendPos = self.settings.value(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.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())
profile1Colour = str(self.preferences['Sample 1 colour'].name())
profile2Colour = str(self.preferences['Sample 2 colour'].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, statsResults.confIntervMethod.bRatio)
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')
if statsResults.multCompCorrection.method != 'No correction':
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'
seqs1 = statsResults.getColumn('Seq1')
seqs2 = statsResults.getColumn('Seq2')
parentSeqs1 = statsResults.getColumn('ParentalSeq1')
parentSeqs2 = statsResults.getColumn('ParentalSeq2')
# *** Truncate feature labels
highlightedFeatures = list(
self.preferences['Highlighted sample 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] + '...'
# *** Adjust effect size for axis scale
dominateInSample2 = []
percentage1 = []
percentage2 = []
for i in xrange(0, len(effectSizes)):
percentage1.append(float(seqs1[i]) * 100 / parentSeqs1[i])
percentage2.append(float(seqs2[i]) * 100 / parentSeqs2[i])
if statsResults.confIntervMethod.bRatio:
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
if self.percentageOrSeqCount == 'Proportion (%)':
# plot percentage
axNumSeq.barh(np.arange(len(features)) + 0.0,
percentage1,
height=0.3,
color=profile1Colour,
zorder=10,
ecolor='black')
axNumSeq.barh(np.arange(len(features)) - 0.3,
percentage2,
height=0.3,
color=profile2Colour,
zorder=10,
ecolor='black')
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(self.percentageOrSeqCount)
maxPercentage = max(max(percentage1), max(percentage2))
axNumSeq.set_xticks([0, maxPercentage])
axNumSeq.set_xlim([0, maxPercentage * 1.05])
maxPercentageStr = '%.1f' % maxPercentage
axNumSeq.set_xticklabels(['0.0', maxPercentageStr])
else:
# plot sequence count
axNumSeq.barh(np.arange(len(features)) + 0.0,
seqs1,
height=0.3,
color=profile1Colour,
zorder=10,
ecolor='black')
axNumSeq.barh(np.arange(len(features)) - 0.3,
seqs2,
height=0.3,
color=profile2Colour,
zorder=10,
ecolor='black')
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(self.percentageOrSeqCount)
maxSeqs = max(max(seqs1), max(seqs2))
axNumSeq.set_xticks([0, maxSeqs])
axNumSeq.set_xlim([0, maxSeqs * 1.05])
axNumSeq.set_xticklabels([0, str(maxSeqs)])
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=profile1Colour,
mec='black',
ecolor='black',
zorder=10)
effectSizesSample2 = [
effectSizes[value] for value in dominateInSample2
]
axErrorbar.plot(effectSizesSample2,
dominateInSample2,
ls='',
marker='o',
ms=markerSize,
mfc=profile2Colour,
mec='black',
zorder=100)
if statsResults.confIntervMethod.bRatio:
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(statsResults.confIntervMethod.plotLabel)
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 highlightedFeatures:
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
for loc, spine in axRight.spines.iteritems():
spine.set_color('none')
# *** Legend
# *** Legend
if self.legendPos != -1:
legend1 = Rectangle((0, 0), 1, 1, fc=profile1Colour)
legend2 = Rectangle((0, 0), 1, 1, fc=profile2Colour)
legend = self.fig.legend([legend1, legend2],
(statsResults.profile.sampleNames[0],
statsResults.profile.sampleNames[1]),
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.cboPercentageOrSeqCount.setEnabled(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.cboPercentageOrSeqCount.setCurrentIndex(
self.configDlg.ui.cboPercentageOrSeqCount.findText(
self.percentageOrSeqCount))
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.percentageOrSeqCount = self.configDlg.ui.cboPercentageOrSeqCount.currentText(
)
# 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(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/row height',
self.figHeightPerRow)
self.settings.setValue(self.name + '/field', self.sortingField)
self.settings.setValue(self.name + '/sequences subplot',
self.bShowBarPlot)
self.settings.setValue(self.name + '/p-value labels',
self.bShowPValueLabels)
self.settings.setValue(self.name + '/show corrected p-values',
self.bShowCorrectedPvalues)
self.settings.setValue(self.name + 'use custom limits',
self.bCustomLimits)
self.settings.setValue(self.name + '/minimum', self.minX)
self.settings.setValue(self.name + '/maximum', self.maxX)
self.settings.setValue(self.name + '/marker size', self.markerSize)
self.settings.setValue(self.name + '/percentage or seq count',
self.percentageOrSeqCount)
self.settings.setValue(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_pValueHistogramDialog)
self.connect(self.configDlg.ui.btnXmax, QtCore.SIGNAL('clicked()'),
self.setXaxisMax)
self.configDlg.ui.cboFieldToPlot.setCurrentIndex(
self.configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.chkShowInset.setChecked(self.bShowInset)
self.configDlg.ui.spinInsetWidth.setValue(self.insetWidth)
self.configDlg.ui.spinInsetHeight.setValue(self.insetHeight)
self.configDlg.ui.spinInsetBinWidth.setValue(self.insetBinWidth)
self.configDlg.ui.spinXlimit.setValue(self.xLimit)
self.configDlg.ui.chkInsetLogScale.setChecked(self.insetLogScale)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.fieldToPlot = self.configDlg.ui.cboFieldToPlot.currentText()
self.bShowInset = self.configDlg.ui.chkShowInset.isChecked()
self.insetWidth = self.configDlg.ui.spinInsetWidth.value()
self.insetHeight = self.configDlg.ui.spinInsetHeight.value()
self.insetBinWidth = self.configDlg.ui.spinInsetBinWidth.value()
self.xLimit = self.configDlg.ui.spinXlimit.value()
self.insetLogScale = self.configDlg.ui.chkInsetLogScale.isChecked()
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/field to plot',
self.fieldToPlot)
self.settings.setValue(self.name + '/histogram log scale',
self.yAxisLogScale)
self.settings.setValue(self.name + '/histogram bin width',
self.binWidth)
self.settings.setValue(self.name + '/show inset', self.bShowInset)
self.settings.setValue(self.name + '/inset width %',
self.insetWidth)
self.settings.setValue(self.name + '/inset height %',
self.insetHeight)
self.settings.setValue(self.name + '/inset log scale',
self.insetLogScale)
self.settings.setValue(self.name + '/inset bin width',
self.insetBinWidth)
self.settings.setValue(self.name + '/inset x-axis limit',
self.xLimit)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
self.statsResults = statsResults
configDlg = ConfigureDialog(Ui_BarConfigDialog)
configDlg.ui.cboFieldToPlot.clear()
configDlg.ui.cboFieldToPlot.addItem('Effect size')
configDlg.ui.cboFieldToPlot.addItem('Number of sequences')
configDlg.ui.cboFieldToPlot.addItem('Number of parental sequences')
configDlg.ui.cboFieldToPlot.addItem('p-values')
configDlg.ui.cboFieldToPlot.addItem('p-values (corrected)')
configDlg.ui.cboFieldToPlot.addItem('Proportion of sequences (%)')
configDlg.ui.cboFieldToPlot.setCurrentIndex(configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
configDlg.ui.chkSort.setChecked(self.bSortFeatures)
configDlg.ui.spinFigWidth.setValue(self.figWidth)
configDlg.ui.spinFigRowHeight.setValue(self.figHeightPerRow)
# legend position
if self.legendPos == 0:
configDlg.ui.radioLegendPosBest.setChecked(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)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.fieldToPlot = str(configDlg.ui.cboFieldToPlot.currentText())
self.bSortFeatures = configDlg.ui.chkSort.isChecked()
self.figWidth = configDlg.ui.spinFigWidth.value()
self.figHeightPerRow = configDlg.ui.spinFigRowHeight.value()
# legend position
self.bShowLegend = True
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.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/row height', self.figHeightPerRow)
self.settings.setValue(self.name + '/field to plot', self.fieldToPlot)
self.settings.setValue(self.name + '/legend position', self.legendPos)
self.settings.setValue(self.name + '/sort values', self.bSortFeatures)
self.plot(profile, statsResults)
class pValueHistogram(AbstractSamplePlotPlugin):
'''
p-value histogram plot.
'''
def __init__(self, preferences, parent=None):
AbstractSamplePlotPlugin.__init__(self, preferences, parent)
self.preferences = preferences
self.name = 'p-value histogram'
self.type = 'Statistical'
self.settings = preferences['Settings']
self.figWidth = self.settings.value(self.name + '/width',
7.0).toDouble()[0]
self.figHeight = self.settings.value(self.name + '/height',
7.0).toDouble()[0]
self.fieldToPlot = self.settings.value(
self.name + '/field to plot', 'p-values (corrected)').toString()
self.yAxisLogScale = self.settings.value(
self.name + '/histogram log scale', False).toBool()
self.binWidth = self.settings.value(self.name + '/histogram bin width',
0.01).toDouble()[0]
self.bShowInset = self.settings.value(self.name + '/show inset',
True).toBool()
self.insetWidth = self.settings.value(self.name + '/inset width %',
60.0).toDouble()[0]
self.insetHeight = self.settings.value(self.name + '/inset height %',
60.0).toDouble()[0]
self.insetLogScale = self.settings.value(
self.name + '/inset log scale', False).toBool()
self.insetBinWidth = self.settings.value(
self.name + '/inset bin width', 0.002).toDouble()[0]
self.xLimit = self.settings.value(self.name + '/inset x-axis limit',
0.05).toDouble()[0]
def mirrorProperties(self, plotToCopy):
self.name = plotToCopy.name
self.figWidth = plotToCopy.figWidth
self.figHeight = plotToCopy.figHeight
self.yAxisLogScale = plotToCopy.yAxisLogScale
self.fieldToPlot = plotToCopy.fieldToPlot
self.bShowInset = plotToCopy.bShowInset
self.insetWidth = plotToCopy.insetWidth
self.insetHeight = plotToCopy.insetHeight
self.insetBinWidth = plotToCopy.insetBinWidth
self.xLimit = plotToCopy.xLimit
self.insetLogScale = plotToCopy.insetLogScale
def plot(self, profile, statsResults):
if len(statsResults.activeData) <= 0:
self.emptyAxis()
return
axesColour = str(self.preferences['Axes colour'].name())
# *** Get data to plot
if self.fieldToPlot == 'p-values':
data = statsResults.getColumn('pValues')
xLabel = 'p-value'
elif self.fieldToPlot == 'p-values (corrected)':
data = statsResults.getColumn('pValuesCorrected')
xLabel = 'p-value (corrected)'
# *** Set size of figure
self.fig.clear()
self.fig.set_size_inches(self.figWidth, self.figHeight)
heightBottomLabels = 0.4 # inches
widthSideLabel = 0.5 # inches
padding = 0.2 # inches
axesHist = self.fig.add_axes([widthSideLabel/self.figWidth,heightBottomLabels/self.figHeight,\
1.0-(widthSideLabel+padding)/self.figWidth,\
1.0-(heightBottomLabels+padding)/self.figHeight])
# *** Histogram plot
bins = [0.0]
binWidth = self.binWidth
binEnd = binWidth
while binEnd <= 1.0:
bins.append(binEnd)
binEnd += binWidth
n, bins, patch = axesHist.hist(data,
bins=bins,
log=self.yAxisLogScale,
color=(0.5, 0.5, 0.5))
axesHist.set_xlabel(xLabel)
axesHist.set_ylabel('Number of features')
# *** Prettify plot
for a in axesHist.yaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for a in axesHist.xaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for line in axesHist.yaxis.get_ticklines():
line.set_color(axesColour)
for line in axesHist.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in axesHist.spines.iteritems():
if loc in ['right', 'top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
# *** Plot inset
if self.bShowInset:
bins = [0.0]
binWidth = self.insetBinWidth
binEnd = binWidth
while binEnd <= self.xLimit:
bins.append(binEnd)
binEnd += binWidth
widthStr = str(self.insetWidth) + '%'
heightStr = str(self.insetHeight) + '%'
axins = inset_axes(axesHist,
width=widthStr,
height=heightStr,
loc=1)
filteredData = [d for d in data if d <= self.xLimit]
if filteredData:
n, bins, patch = axins.hist(filteredData,
bins=bins,
log=self.insetLogScale,
color=(0.5, 0.5, 0.5))
axins.set_xlim(0, self.xLimit)
# *** Prettify inset
for a in axins.yaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for a in axins.xaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for line in axins.yaxis.get_ticklines():
line.set_color(axesColour)
for line in axins.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in axins.spines.iteritems():
if loc in ['right', 'top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
self.updateGeometry()
self.draw()
def configure(self, profile, statsResults):
self.statsResults = statsResults
self.configDlg = ConfigureDialog(Ui_pValueHistogramDialog)
self.connect(self.configDlg.ui.btnXmax, QtCore.SIGNAL('clicked()'),
self.setXaxisMax)
self.configDlg.ui.cboFieldToPlot.setCurrentIndex(
self.configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.chkShowInset.setChecked(self.bShowInset)
self.configDlg.ui.spinInsetWidth.setValue(self.insetWidth)
self.configDlg.ui.spinInsetHeight.setValue(self.insetHeight)
self.configDlg.ui.spinInsetBinWidth.setValue(self.insetBinWidth)
self.configDlg.ui.spinXlimit.setValue(self.xLimit)
self.configDlg.ui.chkInsetLogScale.setChecked(self.insetLogScale)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.fieldToPlot = self.configDlg.ui.cboFieldToPlot.currentText()
self.bShowInset = self.configDlg.ui.chkShowInset.isChecked()
self.insetWidth = self.configDlg.ui.spinInsetWidth.value()
self.insetHeight = self.configDlg.ui.spinInsetHeight.value()
self.insetBinWidth = self.configDlg.ui.spinInsetBinWidth.value()
self.xLimit = self.configDlg.ui.spinXlimit.value()
self.insetLogScale = self.configDlg.ui.chkInsetLogScale.isChecked()
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/field to plot',
self.fieldToPlot)
self.settings.setValue(self.name + '/histogram log scale',
self.yAxisLogScale)
self.settings.setValue(self.name + '/histogram bin width',
self.binWidth)
self.settings.setValue(self.name + '/show inset', self.bShowInset)
self.settings.setValue(self.name + '/inset width %',
self.insetWidth)
self.settings.setValue(self.name + '/inset height %',
self.insetHeight)
self.settings.setValue(self.name + '/inset log scale',
self.insetLogScale)
self.settings.setValue(self.name + '/inset bin width',
self.insetBinWidth)
self.settings.setValue(self.name + '/inset x-axis limit',
self.xLimit)
self.plot(profile, statsResults)
def setXaxisMax(self):
# *** Get data to plot
if self.configDlg.ui.cboFieldToPlot.currentText() == 'p-values':
data = self.statsResults.getColumn('pValues')
else:
data = self.statsResults.getColumn('pValuesCorrected')
self.configDlg.ui.spinXlimit.setValue(max(data))
def configure(self, profile, statsResults):
self.profile = profile
self.configDlg = ConfigureDialog(Ui_SeqHistogramDialog)
self.connect(self.configDlg.ui.chkCustomBinWidth, QtCore.SIGNAL('toggled(bool)'), self.changeCustomBinWidth)
self.connect(self.configDlg.ui.chkCustomXaxis, QtCore.SIGNAL('toggled(bool)'), self.changeCustomXaxis)
self.connect(self.configDlg.ui.btnXmin, QtCore.SIGNAL('clicked()'), self.setXaxisMin)
self.connect(self.configDlg.ui.btnXmax, QtCore.SIGNAL('clicked()'), self.setXaxisMax)
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.chkCustomBinWidth.setChecked(self.bCustomBinWidth)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.chkCustomXaxis.setChecked(self.bCustomXaxis)
self.configDlg.ui.spinXmin.setValue(self.xLimitLeft)
self.configDlg.ui.spinXmax.setValue(self.xLimitRight)
self.changeCustomBinWidth()
self.changeCustomXaxis()
# legend position
if self.legendPos == 0:
self.configDlg.ui.radioLegendPosBest.setDown(True)
elif self.legendPos == 1:
self.configDlg.ui.radioLegendPosUpperRight.setChecked(True)
elif self.legendPos == 7:
self.configDlg.ui.radioLegendPosCentreRight.setChecked(True)
elif self.legendPos == 4:
self.configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 2:
self.configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 6:
self.configDlg.ui.radioLegendPosCentreLeft.setChecked(True)
elif self.legendPos == 3:
self.configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
else:
self.configDlg.ui.radioLegendPosNone.setChecked(True)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.bCustomBinWidth = self.configDlg.ui.chkCustomBinWidth.isChecked()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.bCustomXaxis = self.configDlg.ui.chkCustomXaxis.isChecked()
self.xLimitLeft = self.configDlg.ui.spinXmin.value()
self.xLimitRight = self.configDlg.ui.spinXmax.value()
# legend position
if self.configDlg.ui.radioLegendPosBest.isChecked() == True:
self.legendPos = 0
elif self.configDlg.ui.radioLegendPosUpperRight.isChecked() == True:
self.legendPos = 1
elif self.configDlg.ui.radioLegendPosCentreRight.isChecked() == True:
self.legendPos = 7
elif self.configDlg.ui.radioLegendPosLowerRight.isChecked() == True:
self.legendPos = 4
elif self.configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif self.configDlg.ui.radioLegendPosCentreLeft.isChecked() == True:
self.legendPos = 6
elif self.configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
else:
self.legendPos = -1
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/custom bin width', self.bCustomBinWidth)
self.settings.setValue(self.name + '/bin width', self.binWidth)
self.settings.setValue(self.name + '/log scale', self.yAxisLogScale)
self.settings.setValue(self.name + '/custom x-axis extents', self.bCustomXaxis)
self.settings.setValue(self.name + '/min value', self.xLimitLeft)
self.settings.setValue(self.name + '/max value', self.xLimitRight)
self.settings.setValue(self.name + '/legend position', self.legendPos)
self.plot(profile, statsResults)
