Package: esetVis 1.33.0

Laure Cougnaud

esetVis: Visualizations of expressionSet Bioconductor object

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.

Authors:Laure Cougnaud <[email protected]>

esetVis_1.33.0.tar.gz
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esetVis.pdf |esetVis.html✨
esetVis/json (API)
NEWS

# Install 'esetVis' in R:

install.packages('esetVis', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:esetVis-1.33.0(bioc 3.21)esetVis-1.32.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

visualization datarepresentation dimensionreduction principalcomponent pathways

3.60 score 6 scripts 205 downloads 11 exports 51 dependencies

Last updated 2 months agofrom:84fc5bdd40. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 23 2024
R-4.5-win	NOTE	Nov 23 2024
R-4.5-linux	NOTE	Nov 23 2024
R-4.4-win	NOTE	Nov 23 2024
R-4.4-mac	NOTE	Nov 23 2024
R-4.3-win	NOTE	Nov 23 2024
R-4.3-mac	NOTE	Nov 23 2024

Exports:esetLda esetPlot esetPlotInteractive esetPlotWrapper esetSpectralMap esetTsne getGeneSetsForPlot ggplotEsetPlot ggvisEsetPlot plotEset plotlyEsetPlot

Dependencies:AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 bitops blob cachem caTools cli cpp11 crayon curl DBI fastmap generics GenomeInfoDb GenomeInfoDbData glue gplots gtools hexbin httr IRanges jsonlite KEGGREST KernSmooth lattice lifecycle MASS memoise mime MLP mpm openssl pkgconfig plogr png R6 Rcpp rlang RSQLite Rtsne S4Vectors sys UCSC.utils vctrs XVector zlibbioc

Vignette of the esetVis package

Laure Cougnaud

Rendered fromesetVis-vignette.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-01-02
Started: 2016-06-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
plot a biplot of a linear discriminant analysis of an eSet object	esetLda
wrapper for biplot of features/samples contained in a eSet object	esetPlotWrapper
plot a spectral map biplot of an eSet.	esetSpectralMap
plot a t-SNE of an eSet object	esetTsne
get gene sets for plot of eSet object.	getGeneSetsForPlot
a S4 class to represent 'ggplot' plots	ggplotEsetPlot ggplotEsetPlot-class