Visualizations of expressionSet Bioconductor object

---

Documentation for package ‘esetVis’ version 1.26.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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