예제 #1
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	def __init__(self, preferences, parent=None):
		AbstractGroupPlotPlugin.__init__(self, preferences, parent)


		self.discreteColourMap = mpl.colors.ListedColormap([(141 / 255.0, 211 / 255.0, 199 / 255.0), (255 / 255.0, 255 / 255.0, 179 / 255.0), \
														(190 / 255.0, 186 / 255.0, 218 / 255.0), (251 / 255.0, 128 / 255.0, 114 / 255.0), \
														(128 / 255.0, 177 / 255.0, 211 / 255.0), (253 / 255.0, 180 / 255.0, 98 / 255.0), \
														(179 / 255.0, 222 / 255.0, 105 / 255.0), (252 / 255.0, 205 / 255.0, 229 / 255.0), \
														(217 / 255.0, 217 / 255.0, 217 / 255.0), (188 / 255.0, 128 / 255.0, 189 / 255.0), \
														(204 / 255.0, 235 / 255.0, 197 / 255.0), (255 / 255.0, 237 / 255.0, 111 / 255.0)])

		self.preferences = preferences

		self.name = 'Heatmap plot'
		self.type = 'Exploratory'

		self.bPlotFeaturesIndividually = False

		self.settings = preferences['Settings']
		self.fieldToPlot = self.settings.value('group: ' + self.name + '/field to plot', 'Proportion of sequences (%)').toString()
		self.bPlotOnlyActiveFeatures = self.settings.value('group: ' + self.name + '/plot only active features', False).toBool()
		self.figWidth = self.settings.value('group: ' + self.name + '/width', 7.0).toDouble()[0]
		self.figHeight = self.settings.value('group: ' + self.name + '/height', 7.0).toDouble()[0]
		self.sortColMethod = self.settings.value('group: ' + self.name + '/sort col method', 'Average neighbour (UPGMA)').toString()
		self.sortRowMethod = self.settings.value('group: ' + self.name + '/sort row method', 'Average neighbour (UPGMA)').toString()
		self.bShowColDendrogram = self.settings.value('group: ' + self.name + '/show col dendrogram', True).toBool()
		self.bShowRowDendrogram = self.settings.value('group: ' + self.name + '/show row dendrogram', True).toBool()
		self.colourmap = self.settings.value('group: ' + self.name + '/colourmap', 'Blues').toString()
		self.legendPos = self.settings.value('group: ' + self.name + '/legend position', 3).toInt()[0]
		self.clusteringColThreshold = self.settings.value('group: ' + self.name + '/clustering col threshold', 0.75).toDouble()[0]
		self.clusteringRowThreshold = self.settings.value('group: ' + self.name + '/clustering row threshold', 0.75).toDouble()[0]
		self.dendrogramHeight = self.settings.value('group: ' + self.name + '/dendrogram col height', 1.5).toDouble()[0]
		self.dendrogramWidth = self.settings.value('group: ' + self.name + '/dendrogram row width', 1.5).toDouble()[0]
예제 #2
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    def __init__(self, preferences, parent=None):
        AbstractGroupPlotPlugin.__init__(self, preferences, parent)
        self.preferences = preferences

        self.name = 'Scatter plot'
        self.type = 'Exploratory'
        self.bSupportsHighlight = True
        self.bPlotFeaturesIndividually = False

        self.settings = preferences['Settings']
        self.figWidth = self.settings.value('group: ' + self.name + '/width',
                                            7.0).toDouble()[0]
        self.figHeight = self.settings.value('group: ' + self.name + '/height',
                                             7.0).toDouble()[0]
        self.spreadMethod = self.settings.value(
            'group: ' + self.name + '/spread method',
            '2nd and 98th percentile').toString()
        self.numBins = self.settings.value('group: ' + self.name + '/bins',
                                           30).toInt()[0]
        self.histogramSize = self.settings.value(
            'group: ' + self.name + '/bin size', 0.5).toDouble()[0]
        self.bShowHistograms = self.settings.value(
            'group: ' + self.name + '/show histograms', True).toBool()
        self.markerSize = self.settings.value(
            'group: ' + self.name + '/marker size', 20).toInt()[0]
        self.bShowR2 = self.settings.value('group: ' + self.name + '/show R2',
                                           True).toBool()
예제 #3
0
파일: pcaPlot.py 프로젝트: zhaoxia413/STAMP
    def __init__(self, preferences, parent=None):
        AbstractGroupPlotPlugin.__init__(self, preferences, parent)
        self.preferences = preferences

        self.name = 'PCA plot'
        self.type = 'Exploratory'

        self.bPlotFeaturesIndividually = False

        self.settings = preferences['Settings']
        self.figWidth = self.settings.value('group: ' + self.name + '/width',
                                            7.0).toDouble()[0]
        self.figHeight = self.settings.value('group: ' + self.name + '/height',
                                             6.0).toDouble()[0]
        self.bFixedPixelsPerUnitDistance = self.settings.value(
            'group: ' + self.name + '/fixed pixels per unit distance',
            True).toBool()
        self.markerSize = self.settings.value(
            'group: ' + self.name + '/marker size', 30).toInt()[0]
        self.bRotateLabels = self.settings.value(
            'group: ' + self.name + '/rotate pc3 labels', True).toBool()
        self.bShowPC1vsPC3 = self.settings.value(
            'group: ' + self.name + '/showPC1vsPC3', True).toBool()
        self.bShowPC3vsPC2 = self.settings.value(
            'group: ' + self.name + '/showPC3vsPC2', True).toBool()
        self.legendPos = self.settings.value(
            'group: ' + self.name + '/legend position', -1).toInt()[0]
        self.bUniqueShapes = self.settings.value(
            'group: ' + self.name + '/unique shapes', True).toBool()
예제 #4
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    def __init__(self, preferences, parent=None):
        AbstractGroupPlotPlugin.__init__(self, preferences, parent)


        self.discreteColourMap = mpl.colors.ListedColormap([(141 / 255.0, 211 / 255.0, 199 / 255.0), (255 / 255.0, 255 / 255.0, 179 / 255.0), \
                    (190 / 255.0, 186 / 255.0, 218 / 255.0), (251 / 255.0, 128 / 255.0, 114 / 255.0), \
                    (128 / 255.0, 177 / 255.0, 211 / 255.0), (253 / 255.0, 180 / 255.0, 98 / 255.0), \
                    (179 / 255.0, 222 / 255.0, 105 / 255.0), (252 / 255.0, 205 / 255.0, 229 / 255.0), \
                    (217 / 255.0, 217 / 255.0, 217 / 255.0), (188 / 255.0, 128 / 255.0, 189 / 255.0), \
                    (204 / 255.0, 235 / 255.0, 197 / 255.0), (255 / 255.0, 237 / 255.0, 111 / 255.0)])

        self.preferences = preferences

        self.name = 'Heatmap plot'
        self.type = 'Exploratory'

        self.bPlotFeaturesIndividually = False

        self.settings = preferences['Settings']
        self.fieldToPlot = self.settings.value(
            'group: ' + self.name + '/field to plot',
            'Proportion of sequences (%)').toString()
        self.bPlotOnlyActiveFeatures = self.settings.value(
            'group: ' + self.name + '/plot only active features',
            False).toBool()
        self.figWidth = self.settings.value('group: ' + self.name + '/width',
                                            7.0).toDouble()[0]
        self.figHeight = self.settings.value('group: ' + self.name + '/height',
                                             7.0).toDouble()[0]
        self.sortColMethod = self.settings.value(
            'group: ' + self.name + '/sort col method',
            'Average neighbour (UPGMA)').toString()
        self.sortRowMethod = self.settings.value(
            'group: ' + self.name + '/sort row method',
            'Average neighbour (UPGMA)').toString()
        self.bShowColDendrogram = self.settings.value(
            'group: ' + self.name + '/show col dendrogram', True).toBool()
        self.bShowRowDendrogram = self.settings.value(
            'group: ' + self.name + '/show row dendrogram', True).toBool()
        self.colourmap = self.settings.value(
            'group: ' + self.name + '/colourmap', 'Blues').toString()
        self.legendPos = self.settings.value(
            'group: ' + self.name + '/legend position', 3).toInt()[0]
        self.clusteringColThreshold = self.settings.value(
            'group: ' + self.name + '/clustering col threshold',
            0.75).toDouble()[0]
        self.clusteringRowThreshold = self.settings.value(
            'group: ' + self.name + '/clustering row threshold',
            0.75).toDouble()[0]
        self.dendrogramHeight = self.settings.value(
            'group: ' + self.name + '/dendrogram col height',
            1.5).toDouble()[0]
        self.dendrogramWidth = self.settings.value(
            'group: ' + self.name + '/dendrogram row width', 1.5).toDouble()[0]
예제 #5
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파일: BoxPlot.py 프로젝트: IUEayhu/STAMP
	def __init__(self, preferences, parent=None):
		AbstractGroupPlotPlugin.__init__(self, preferences, parent)
		self.preferences = preferences
	 
		self.name = 'Box plot'
		self.type = 'Exploratory'
		
		self.settings = preferences['Settings']
		self.figWidth = self.settings.value('group: ' + self.name + '/width', 7.0).toDouble()[0]
		self.figHeight = self.settings.value('group: ' + self.name + '/height', 7.0).toDouble()[0]
		self.fieldToPlot = self.settings.value('group: ' + self.name + '/field to plot', 'Proportion of sequences (%)').toString()
		self.bShowAverages = self.settings.value('group: ' + self.name + '/show averages', True).toBool()
		self.bShowPvalue = self.settings.value('group: ' + self.name + '/show p-value', True).toBool()
예제 #6
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	def __init__(self, preferences, parent=None):
		AbstractGroupPlotPlugin.__init__(self, preferences, parent)
		self.preferences = preferences

		self.name = 'Bar plot'
		self.type = 'Exploratory'

		self.settings = preferences['Settings']
		self.figColWidth = self.settings.value('group: ' + self.name + '/column width', 0.2).toDouble()[0]
		self.figHeight = self.settings.value('group: ' + self.name + '/height', 6.0).toDouble()[0]
		self.fieldToPlot = self.settings.value('group: ' + self.name + '/field to plot', 'Proportion of sequences (%)').toString()
		self.bShowAverages = self.settings.value('group: ' + self.name + '/show averages', True).toBool()
		self.legendPos = self.settings.value('group: ' + self.name + '/legend position', -1).toInt()[0]
		self.bShowPvalue = self.settings.value('group: ' + self.name + '/show p-value', True).toBool()
예제 #7
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	def __init__(self, preferences, parent=None):
		AbstractGroupPlotPlugin.__init__(self, preferences, parent)
		self.preferences = preferences

		self.name = 'Scatter plot'
		self.type = 'Exploratory'
		self.bSupportsHighlight = True
		self.bPlotFeaturesIndividually = False
		
		self.settings = preferences['Settings']
		self.figWidth = self.settings.value('group: ' + self.name + '/width', 7.0).toDouble()[0]
		self.figHeight = self.settings.value('group: ' + self.name + '/height', 7.0).toDouble()[0]
		self.spreadMethod = self.settings.value('group: ' + self.name + '/spread method', '2nd and 98th percentile').toString()
		self.numBins = self.settings.value('group: ' + self.name + '/bins', 30).toInt()[0]
		self.histogramSize = self.settings.value('group: ' + self.name + '/bin size', 0.5).toDouble()[0]
		self.bShowHistograms = self.settings.value('group: ' + self.name + '/show histograms', True).toBool()
		self.markerSize = self.settings.value('group: ' + self.name + '/marker size', 20).toInt()[0]
		self.bShowR2 = self.settings.value('group: ' + self.name + '/show R2', True).toBool()
예제 #8
0
파일: pcaPlot.py 프로젝트: IUEayhu/STAMP
	def __init__(self, preferences, parent=None):
		AbstractGroupPlotPlugin.__init__(self, preferences, parent)
		self.preferences = preferences

		self.name = 'PCA plot'
		self.type = 'Exploratory'
		
		self.bPlotFeaturesIndividually = False
		
		self.settings = preferences['Settings']
		self.figWidth = self.settings.value('group: ' + self.name + '/width', 7.0).toDouble()[0]
		self.figHeight = self.settings.value('group: ' + self.name + '/height', 6.0).toDouble()[0]
		self.bFixedPixelsPerUnitDistance = self.settings.value('group: ' + self.name + '/fixed pixels per unit distance', True).toBool()
		self.markerSize = self.settings.value('group: ' + self.name + '/marker size', 30).toInt()[0]
		self.bRotateLabels = self.settings.value('group: ' + self.name + '/rotate pc3 labels', True).toBool()
		self.bShowPC1vsPC3 = self.settings.value('group: ' + self.name + '/showPC1vsPC3', True).toBool()
		self.bShowPC3vsPC2 = self.settings.value('group: ' + self.name + '/showPC3vsPC2', True).toBool()
		self.legendPos = self.settings.value('group: ' + self.name + '/legend position', -1).toInt()[0]
		self.bUniqueShapes = self.settings.value('group: ' + self.name + '/unique shapes', True).toBool()
예제 #9
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	def __init__(self, preferences, parent=None):
		AbstractGroupPlotPlugin.__init__(self, preferences, parent)
		
		self.name = 'Extended error bar'
		self.type = 'Statistical'
		
		self.bSupportsHighlight = True
		self.bPlotFeaturesIndividually = False
		
		self.settings = preferences['Settings']
		self.figWidth = self.settings.value('group: ' + self.name + '/width', 7.0).toDouble()[0]
		self.figHeightPerRow = self.settings.value('group: ' + self.name + '/row height', 0.2).toDouble()[0]
		self.sortingField = self.settings.value('group: ' + self.name + '/field', 'p-values').toString()
		self.bShowBarPlot = self.settings.value('group: ' + self.name + '/sequences subplot', True).toBool()
		self.bShowPValueLabels = self.settings.value('group: ' + self.name + '/p-value labels', True).toBool()
		self.bShowCorrectedPvalues = self.settings.value('group: ' + self.name + '/show corrected p-values', True).toBool()
		self.bCustomLimits = self.settings.value('group: ' + self.name + '/use custom limits', False).toBool()
		self.minX = self.settings.value('group: ' + self.name + '/minimum', 0.0).toDouble()[0]
		self.maxX = self.settings.value('group: ' + self.name + '/maximum', 1.0).toDouble()[0]
		self.markerSize = self.settings.value('group: ' + self.name + '/marker size', 30).toInt()[0]
		self.bShowStdDev = self.settings.value('group: ' + self.name + '/show std. dev.', False).toBool()
		self.endCapSize = self.settings.value('group: ' + self.name + '/end cap size', 0.0).toInt()[0]
		self.legendPos = self.settings.value('group: ' + self.name + '/legend position', -1).toInt()[0]
예제 #10
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	def __init__(self, preferences, parent=None):
		AbstractGroupPlotPlugin.__init__(self, preferences, parent)
		
		self.name = 'Extended error bar'
		self.type = 'Statistical'
		
		self.bSupportsHighlight = True
		self.bPlotFeaturesIndividually = False
		
		self.settings = preferences['Settings']
		self.figWidth = self.settings.value('group: ' + self.name + '/width', 7.0).toDouble()[0]
		self.figHeightPerRow = self.settings.value('group: ' + self.name + '/row height', 0.2).toDouble()[0]
		self.sortingField = self.settings.value('group: ' + self.name + '/field', 'p-values').toString()
		self.bShowBarPlot = self.settings.value('group: ' + self.name + '/sequences subplot', True).toBool()
		self.bShowPValueLabels = self.settings.value('group: ' + self.name + '/p-value labels', True).toBool()
		self.bShowCorrectedPvalues = self.settings.value('group: ' + self.name + '/show corrected p-values', True).toBool()
		self.bCustomLimits = self.settings.value('group: ' + self.name + '/use custom limits', False).toBool()
		self.minX = self.settings.value('group: ' + self.name + '/minimum', 0.0).toDouble()[0]
		self.maxX = self.settings.value('group: ' + self.name + '/maximum', 1.0).toDouble()[0]
		self.markerSize = self.settings.value('group: ' + self.name + '/marker size', 30).toInt()[0]
		self.bShowStdDev = self.settings.value('group: ' + self.name + '/show std. dev.', False).toBool()
		self.endCapSize = self.settings.value('group: ' + self.name + '/end cap size', 0.0).toInt()[0]
		self.legendPos = self.settings.value('group: ' + self.name + '/legend position', -1).toInt()[0]