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 __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 __init__(self, preferences, parent=None):
AbstractSamplePlotPlugin.__init__(self, preferences, parent)
self.preferences = preferences
self.name = 'Profile bar plot'
self.type = 'Exploratory'
self.settings = preferences['Settings']
self.figColWidth = self.settings.value(self.name + '/column width',
0.25).toDouble()[0]
self.figHeight = self.settings.value(self.name + '/height',
6.0).toDouble()[0]
self.fieldToPlot = self.settings.value(
self.name + '/field to plot',
'Proportion of sequences (%)').toString()
self.legendPos = self.settings.value(self.name + '/legend position',
0).toInt()[0]
self.bShowCIs = self.settings.value(self.name + '/show cis',
True).toBool()
self.endCapSize = self.settings.value(self.name + '/end cap size',
0).toInt()[0]
self.numFeaturesToShow = self.settings.value(
self.name + '/features to show', 50).toInt()[0]
self.barWidth = self.settings.value(self.name + '/bar width (%)',
80).toDouble()[0]
self.bShowPvalue = self.settings.value(self.name + '/show p-value',
True).toBool()
self.pValueThreshold = self.settings.value(
self.name + '/p-value threshold', 0.05).toDouble()[0]
self.bOnlyActiveFeatures = self.settings.value(
self.name + '/only active features', True).toBool()
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 __init__(self, preferences, parent=None): AbstractSamplePlotPlugin.__init__(self, preferences, parent) self.preferences = preferences self.name = 'My scatter plot' self.figWidth = 7.0 self.figHeight = 7.0 self.sampleName1 = '' self.sampleName2 = ''
def __init__(self, preferences, parent=None):
AbstractSamplePlotPlugin.__init__(self, preferences, parent)
self.preferences = preferences
self.name = 'My scatter plot'
self.figWidth = 7.0
self.figHeight = 7.0
self.sampleName1 = ''
self.sampleName2 = ''
def __init__(self, preferences, parent=None): AbstractSamplePlotPlugin.__init__(self, preferences, parent) self.preferences = preferences self.name = 'Bar plot' 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.fieldToPlot = self.settings.value(self.name + '/field to plot', 'Proportion of sequences (%)').toString() self.legendPos = self.settings.value(self.name + '/legend position', 0).toInt()[0] self.bSortFeatures = self.settings.value(self.name + '/sort values', True).toBool()
def __init__(self, preferences, parent=None): AbstractSamplePlotPlugin.__init__(self, preferences, parent) self.preferences = preferences self.name = 'Scatter plot' 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.bShowCIs = self.settings.value(self.name + '/show CIs', True).toBool() self.numBins = self.settings.value(self.name + '/bins', 30).toInt()[0] self.histogramSize = self.settings.value(self.name + '/bin size', 0.5).toDouble()[0] self.bShowHistograms = self.settings.value(self.name + '/show histograms', True).toBool() self.markerSize = self.settings.value(self.name + '/marker size', 20).toInt()[0] self.bShowR2 = self.settings.value(self.name + '/show R2', True).toBool()
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 __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 __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 __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 __init__(self, preferences, parent=None): AbstractSamplePlotPlugin.__init__(self, preferences, parent) self.preferences = preferences self.name = 'Profile bar plot' self.type = 'Exploratory' self.settings = preferences['Settings'] self.figColWidth = self.settings.value(self.name + '/column width', 0.25).toDouble()[0] self.figHeight = self.settings.value(self.name + '/height', 6.0).toDouble()[0] self.fieldToPlot = self.settings.value(self.name + '/field to plot', 'Proportion of sequences (%)').toString() self.legendPos = self.settings.value(self.name + '/legend position', 0).toInt()[0] self.bShowCIs = self.settings.value(self.name + '/show cis', True).toBool() self.endCapSize = self.settings.value(self.name + '/end cap size', 0).toInt()[0] self.numFeaturesToShow = self.settings.value(self.name + '/features to show', 50).toInt()[0] self.barWidth = self.settings.value(self.name + '/bar width (%)', 80).toDouble()[0] self.bShowPvalue = self.settings.value(self.name + '/show p-value', True).toBool() self.pValueThreshold = self.settings.value(self.name + '/p-value threshold', 0.05).toDouble()[0] self.bOnlyActiveFeatures = self.settings.value(self.name + '/only active features', True).toBool()