Introduction | Example dataset | ExpressionSet object | SummarizedExperiment object | Spectral map: esetSpectralMap | Simple spectral map | Additional sample information | General | Custom size and transparency | Custom gene representation | Label outlying elements | Parameters | Method to select top elements | Package used for static plot | Example | Gene sets annotation | Dimensions of the biplot | Implementation | Interactive spectral map | plotly | ggvis | Tsne: esetTsne | Additional pre-processing step | Linear discriminant analysis: esetLda | All samples | Data sample subset | References
Package: esetVis 1.39.0
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:
esetVis_1.39.0.tar.gz
esetVis_1.39.0.zip(r-4.7)esetVis_1.39.0.zip(r-4.6)esetVis_1.39.0.zip(r-4.5)
esetVis_1.39.0.tgz(r-4.6-any)esetVis_1.39.0.tgz(r-4.5-any)
esetVis_1.39.0.tar.gz(r-4.7-any)esetVis_1.39.0.tar.gz(r-4.6-any)
esetVis_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
esetVis/json (API)
| # Install 'esetVis' in R: |
| install.packages('esetVis', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:esetVis-1.39.0(bioc 3.24)esetVis-1.38.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
visualizationdatarepresentationdimensionreductionprincipalcomponentpathways
Last updated from:268e44c627. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 220 | ||
| linux-devel-x86_64 | NOTE | 312 | ||
| source / vignettes | OK | 290 | ||
| linux-release-x86_64 | NOTE | 315 | ||
| macos-release-arm64 | NOTE | 166 | ||
| macos-oldrel-arm64 | NOTE | 212 | ||
| windows-devel | NOTE | 270 | ||
| windows-release | NOTE | 225 | ||
| windows-oldrel | NOTE | 225 | ||
| wasm-release | OK | 216 |
Exports:esetLdaesetPlotesetPlotInteractiveesetPlotWrapperesetSpectralMapesetTsnegetGeneSetsForPlotggplotEsetPlotggvisEsetPlotplotEsetplotlyEsetPlot
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemcaToolsclicpp11crayoncurlDBIfastmapgenericsgluegplotsgtoolshexbinhttrIRangesjsonliteKEGGRESTKernSmoothlatticelifecycleMASSmemoisemimeMLPmpmopensslpkgconfigpngR6RcpprlangRSQLiteRtsneS4VectorsSeqinfosysvctrsXVector
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 |
