Visualizations of expressionSet Bioconductor object


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Documentation for package ‘esetVis’ version 1.26.1

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characterORexpressionOrCall-class S4 Class Union with character/expression/call
esetLda plot a biplot of a linear discriminant analysis of an eSet object
esetPlot An S4 class to represent 'esetPlot' object expressionSet with visualization data from dimension-reduction methods
esetPlot-class An S4 class to represent 'esetPlot' object expressionSet with visualization data from dimension-reduction methods
esetPlotInteractive a S4 class to represent interactive plots
esetPlotInteractive-class a S4 class to represent interactive plots
esetPlotWrapper wrapper for biplot of features/samples contained in a eSet object
esetSpectralMap plot a spectral map biplot of an eSet.
esetTsne plot a t-SNE of an eSet object
formatManualScale extend manual scale values if required
formatOutput format output of plotEset function
getAxesLimits generic for get axes limits
getAxesLimits-method generic for get axes limits
getCoordGeneSets extract coordinates gene sets
getDataPlotSamplesWithAnnotation get sample data for plot
getDataPlotSamplesWithAnnotation-method get sample data for plot
getGeneSetsForPlot get gene sets for plot of eSet object.
getMethodsInputObjectEsetVis wrapper to extract useful functions, depending if the object is an ExpressionSet or a SummarizedExperiment.
ggPlotEset visualize and esetPlot with the 'ggplot2' package
ggplotEsetPlot a S4 class to represent 'ggplot' plots
ggplotEsetPlot-class a S4 class to represent 'ggplot' plots
ggvisEsetPlot a S4 class for 'ggvis' plot
ggvisEsetPlot-class a S4 class for 'ggvis' plot
ggvisPlotEset visualize and esetPlot with the the 'ggvis' package
initialize-method An S4 class to represent 'esetPlot' object expressionSet with visualization data from dimension-reduction methods
plotEset plot an plotEset object
plotEset-method plot an plotEset object
plotTopElements create 'geom_text' object with top genes/sample/pathways
rbokehEsetPlot a S4 class to represent 'rbokeh' plots
rbokehEsetPlot-class a S4 class to represent 'rbokeh' plots
rbokehPlotEset visualize and esetPlot with the the 'rbokeh' package
setFixElement check if the aesthetic is fixed (e.g. color, shape, size 'palette')
setManualScale check if manual aesthetic should be set
simpleCap capitalize the first letter of a word