# Visualizations of expressionSet Bioconductor object

## Documentation for package ‘esetVis’ version 1.18.0

- 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