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]
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()
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()
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]
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()
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()
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()
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()
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]
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]