Ejemplo n.º 1
0
    def __init__(self, preferences, parent=None):
        AbstractMultiGroupPlotPlugin.__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(
            'multiple group: ' + self.name + '/width', 7.0).toDouble()[0]
        self.figHeight = self.settings.value(
            'multiple group: ' + self.name + '/height', 6.0).toDouble()[0]
        self.bFixedPixelsPerUnitDistance = self.settings.value(
            'multiple group: ' + self.name + '/fixed pixels per unit distance',
            True).toBool()
        self.markerSize = self.settings.value(
            'multiple group: ' + self.name + '/marker size', 30).toInt()[0]
        self.bRotateLabels = self.settings.value(
            'multiple group: ' + self.name + '/rotate pc3 labels',
            True).toBool()
        self.bShowPC1vsPC3 = self.settings.value(
            'multiple group: ' + self.name + '/showPC1vsPC3', True).toBool()
        self.bShowPC3vsPC2 = self.settings.value(
            'multiple group: ' + self.name + '/showPC3vsPC2', True).toBool()
        self.bUniqueShapes = self.settings.value(
            'group: ' + self.name + '/unique shapes', True).toBool()
Ejemplo n.º 2
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	def __init__(self, preferences, parent=None):
		AbstractMultiGroupPlotPlugin.__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('multiple group: ' + self.name + '/field to plot', 'Proportion of sequences (%)').toString()
		self.figWidth = self.settings.value('multiple group: ' + self.name + '/width', 7.0).toDouble()[0]
		self.figHeight = self.settings.value('multiple group: ' + self.name + '/height', 7.0).toDouble()[0]
		self.dendrogramMethod = self.settings.value('multiple group: ' + self.name + '/dendrogram method', 'Average neighbour (UPGMA)').toString()
		self.bShowTopDendrogram = self.settings.value('multiple group: ' + self.name + '/show top dendrogram', True).toBool()
		self.bShowLeftDendrogram = self.settings.value('multiple group: ' + self.name + '/show left dendrogram', True).toBool()
		self.colourmap = self.settings.value('multiple group: ' + self.name + '/colourmap', 'Blue to white to red').toString()
		self.legendPos = self.settings.value('multiple group: ' + self.name + '/legend position', 3).toInt()[0]
		self.clusteringThreshold = self.settings.value('multiple group: ' + self.name + '/clustering threshold', 0.75).toDouble()[0]
		self.dendrogramHeight = self.settings.value('multiple group: ' + self.name + '/dendrogram height', 1.5).toDouble()[0]
		self.dendrogramWidth = self.settings.value('multiple group: ' + self.name + '/dendrogram width', 1.5).toDouble()[0]
Ejemplo n.º 3
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	def __init__(self, preferences, parent=None):
		AbstractMultiGroupPlotPlugin.__init__(self, preferences, parent)
		self.preferences = preferences
	 
		self.name = 'Box plot'
		self.type = 'Exploratory'
		
		self.settings = preferences['Settings']
		self.figWidth = self.settings.value('multiple group: ' + self.name + '/width', 7.0).toDouble()[0]
		self.figHeight = self.settings.value('multiple group: ' + self.name + '/height', 7.0).toDouble()[0]
		self.fieldToPlot = self.settings.value('multiple group: ' + self.name + '/field to plot', 'Proportion of sequences (%)').toString()
		self.bShowAverages = self.settings.value('multiple group: ' + self.name + '/show averages', True).toBool()
		self.bShowPvalue = self.settings.value('multiple group: ' + self.name + '/show p-value', True).toBool()
Ejemplo n.º 4
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	def __init__(self, preferences, parent=None):
		AbstractMultiGroupPlotPlugin.__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('multiple group: ' + self.name + '/width', 7.0).toDouble()[0]
		self.figHeight = self.settings.value('multiple group: ' + self.name + '/height', 6.0).toDouble()[0]
		self.bFixedPixelsPerUnitDistance = self.settings.value('multiple group: ' + self.name + '/fixed pixels per unit distance', True).toBool()
		self.markerSize = self.settings.value('multiple group: ' + self.name + '/marker size', 30).toInt()[0]
		self.bRotateLabels = self.settings.value('multiple group: ' + self.name + '/rotate pc3 labels', True).toBool()
		self.bShowPC1vsPC3 = self.settings.value('multiple group: ' + self.name + '/showPC1vsPC3', True).toBool()
		self.bShowPC3vsPC2 = self.settings.value('multiple group: ' + self.name + '/showPC3vsPC2', True).toBool()
		self.bUniqueShapes = self.settings.value('group: ' + self.name + '/unique shapes', True).toBool()
Ejemplo n.º 5
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    def __init__(self, preferences, parent=None):
        AbstractMultiGroupPlotPlugin.__init__(self, preferences, parent)
        self.preferences = preferences

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

        self.settings = preferences['Settings']
        self.figWidth = self.settings.value(
            'multiple group: ' + self.name + '/width', 7.0).toDouble()[0]
        self.figHeight = self.settings.value(
            'multiple group: ' + self.name + '/height', 7.0).toDouble()[0]
        self.fieldToPlot = self.settings.value(
            'multiple group: ' + self.name + '/field to plot',
            'Proportion of sequences (%)').toString()
        self.bShowAverages = self.settings.value(
            'multiple group: ' + self.name + '/show averages', True).toBool()
        self.bShowPvalue = self.settings.value(
            'multiple group: ' + self.name + '/show p-value', True).toBool()
Ejemplo n.º 6
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    def __init__(self, preferences, parent=None):
        AbstractMultiGroupPlotPlugin.__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("multiple group: " + self.name + "/width", 7.0).toDouble()[0]
        self.figHeight = self.settings.value("multiple group: " + self.name + "/height", 6.0).toDouble()[0]
        self.bFixedPixelsPerUnitDistance = self.settings.value(
            "multiple group: " + self.name + "/fixed pixels per unit distance", True
        ).toBool()
        self.markerSize = self.settings.value("multiple group: " + self.name + "/marker size", 30).toInt()[0]
        self.bRotateLabels = self.settings.value("multiple group: " + self.name + "/rotate pc3 labels", True).toBool()
        self.bShowPC1vsPC3 = self.settings.value("multiple group: " + self.name + "/showPC1vsPC3", True).toBool()
        self.bShowPC3vsPC2 = self.settings.value("multiple group: " + self.name + "/showPC3vsPC2", True).toBool()
        self.bUniqueShapes = self.settings.value("group: " + self.name + "/unique shapes", True).toBool()
Ejemplo n.º 7
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	def __init__(self, preferences, parent=None):
		AbstractMultiGroupPlotPlugin.__init__(self, preferences, parent)
		
		self.name = 'Post-hoc plot'
		self.type = 'Statistical'

		self.bRunPostHocTest = True
		
		self.settings = preferences['Settings']
		self.figWidth = self.settings.value('multiple group: ' + self.name + '/width', 7.0).toDouble()[0]
		self.figHeightPerRow = self.settings.value('multiple group: ' + self.name + '/row height', 0.2).toDouble()[0]
		self.sortingField = self.settings.value('multiple group: ' + self.name + '/field', 'p-values').toString()
		self.bShowBarPlot = self.settings.value('multiple group: ' + self.name + '/sequences subplot', True).toBool()
		self.bShowPValueLabels = self.settings.value('multiple group: ' + self.name + '/p-value labels', True).toBool()
		self.bCustomLimits = self.settings.value('multiple group: ' + self.name + '/use custom limits', False).toBool()
		self.minX = self.settings.value('multiple group: ' + self.name + '/minimum', 0.0).toDouble()[0]
		self.maxX = self.settings.value('multiple group: ' + self.name + '/maximum', 1.0).toDouble()[0]
		self.markerSize = self.settings.value('multiple group: ' + self.name + '/marker size', 30).toInt()[0]
		self.bShowStdDev = self.settings.value('multiple group: ' + self.name + '/show std. dev.', False).toBool()
		self.endCapSize = self.settings.value('multiple group: ' + self.name + '/end cap size', 0.0).toInt()[0]
		self.bPvalueFilter = self.settings.value('multiple group: ' + self.name + '/p-value filter', True).toBool()
Ejemplo n.º 8
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    def __init__(self, preferences, parent=None):
        AbstractMultiGroupPlotPlugin.__init__(self, preferences, parent)

        self.name = 'Post-hoc plot'
        self.type = 'Statistical'

        self.bRunPostHocTest = True

        self.settings = preferences['Settings']
        self.figWidth = self.settings.value(
            'multiple group: ' + self.name + '/width', 7.0).toDouble()[0]
        self.figHeightPerRow = self.settings.value(
            'multiple group: ' + self.name + '/row height', 0.2).toDouble()[0]
        self.sortingField = self.settings.value(
            'multiple group: ' + self.name + '/field', 'p-values').toString()
        self.bShowBarPlot = self.settings.value(
            'multiple group: ' + self.name + '/sequences subplot',
            True).toBool()
        self.bShowPValueLabels = self.settings.value(
            'multiple group: ' + self.name + '/p-value labels', True).toBool()
        self.bCustomLimits = self.settings.value(
            'multiple group: ' + self.name + '/use custom limits',
            False).toBool()
        self.minX = self.settings.value(
            'multiple group: ' + self.name + '/minimum', 0.0).toDouble()[0]
        self.maxX = self.settings.value(
            'multiple group: ' + self.name + '/maximum', 1.0).toDouble()[0]
        self.markerSize = self.settings.value(
            'multiple group: ' + self.name + '/marker size', 30).toInt()[0]
        self.bShowStdDev = self.settings.value(
            'multiple group: ' + self.name + '/show std. dev.',
            False).toBool()
        self.endCapSize = self.settings.value(
            'multiple group: ' + self.name + '/end cap size', 0.0).toInt()[0]
        self.bPvalueFilter = self.settings.value(
            'multiple group: ' + self.name + '/p-value filter', True).toBool()