コード例 #1
0
    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
コード例 #2
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    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]
コード例 #3
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    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]
コード例 #4
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    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]
コード例 #5
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    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]
コード例 #6
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    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 = ''
コード例 #7
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ファイル: MyScatterPlot.py プロジェクト: beiko-lab/STAMP
	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 = ''
コード例 #8
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ファイル: Bar.py プロジェクト: beiko-lab/STAMP
	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()
コード例 #9
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ファイル: ScatterPlot.py プロジェクト: beiko-lab/STAMP
	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()
コード例 #10
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ファイル: SeqHistogram.py プロジェクト: jnesme/STAMP
	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]
コード例 #11
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	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
コード例 #12
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ファイル: ProfileBarPlots.py プロジェクト: beiko-lab/STAMP
	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]
コード例 #13
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ファイル: pValueHistogram.py プロジェクト: beiko-lab/STAMP
	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]
コード例 #14
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    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()
コード例 #15
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ファイル: ExtendedErrorBar.py プロジェクト: beiko-lab/STAMP
	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]
コード例 #16
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ファイル: ScatterPlot.py プロジェクト: mlangill/STAMP
    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()