esetVis: Visualizations of expressionSet Bioconductor object

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Utility functions for visualization of expressionSet (or SummarizedExperiment) Bioconductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available.

Author
Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Date of publication
None
Maintainer
Laure Cougnaud <laure.cougnaud@openanalytics.eu>
License
GPL-3
Version
1.0.1

View on Bioconductor

Man pages

esetLda
plot a biplot of a linear discriminant analysis of an eSet...
esetPlotWrapper
wrapper for biplot of features/samples contained in a eSet...
esetSpectralMap
plot a spectral map biplot of an eSet.
esetTsne
plot a t-SNE of an eSet object
getCoordGeneSets
extract coordinates gene sets
getGeneSetsForPlot
get gene sets for plot of eSet object.
getMethodsInputObjectEsetVis
wrapper to extract useful functions, depending if the object...
plotTopElements
create 'geom_text' object with top genes/sample/pathways

Files in this package

esetVis/DESCRIPTION
esetVis/NAMESPACE
esetVis/R
esetVis/R/esetLda.R
esetVis/R/esetPlotWrapper.R
esetVis/R/esetSpectralMap.R
esetVis/R/esetTsne.R
esetVis/R/getGeneSetsForPlot.R
esetVis/R/getMethodsInputObjectEsetVis.R
esetVis/R/plotTopElements.R
esetVis/build
esetVis/build/vignette.rds
esetVis/inst
esetVis/inst/NEWS
esetVis/inst/doc
esetVis/inst/doc/esetVis-vignette.R
esetVis/inst/doc/esetVis-vignette.Rmd
esetVis/inst/doc/esetVis-vignette.html
esetVis/man
esetVis/man/esetLda.Rd
esetVis/man/esetPlotWrapper.Rd
esetVis/man/esetSpectralMap.Rd
esetVis/man/esetTsne.Rd
esetVis/man/getCoordGeneSets.Rd
esetVis/man/getGeneSetsForPlot.Rd
esetVis/man/getMethodsInputObjectEsetVis.Rd
esetVis/man/plotTopElements.Rd
esetVis/vignettes
esetVis/vignettes/custom.css
esetVis/vignettes/esetVis-vignette.Rmd