esetVis: Visualizations of expressionSet Bioconductor object
Version 1.2.0

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.

AuthorLaure Cougnaud <laure.cougnaud@openanalytics.eu>
Bioconductor views DataRepresentation DimensionReduction Pathways PrincipalComponent Visualization
Date of publicationNone
MaintainerLaure Cougnaud <laure.cougnaud@openanalytics.eu>
LicenseGPL-3
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("esetVis")

Getting started

Vignette of the esetVis package

Popular 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.
plotTopElements: create 'geom_text' object with top genes/sample/pathways
See all...

All man pages Function index File listing

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

Functions

esetLda Man page Source code
esetPlotWrapper Man page Source code
esetSpectralMap Man page Source code
esetTsne Man page Source code
getCoordGeneSets Man page Source code
getGeneSetsForPlot Man page Source code
getMethodsInputObjectEsetVis Man page Source code
plotTopElements Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/esetLda.R
R/esetPlotWrapper.R
R/esetSpectralMap.R
R/esetTsne.R
R/getGeneSetsForPlot.R
R/getMethodsInputObjectEsetVis.R
R/plotTopElements.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/esetVis-vignette.R
inst/doc/esetVis-vignette.Rmd
inst/doc/esetVis-vignette.html
man
man/esetLda.Rd
man/esetPlotWrapper.Rd
man/esetSpectralMap.Rd
man/esetTsne.Rd
man/getCoordGeneSets.Rd
man/getGeneSetsForPlot.Rd
man/getMethodsInputObjectEsetVis.Rd
man/plotTopElements.Rd
vignettes
vignettes/custom.css
vignettes/esetVis-vignette.Rmd
esetVis documentation built on May 20, 2017, 10:51 p.m.

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