Introduction | Installation | Quick start | Loading the package and example data | The basic overlay model | Choosing the foreground and background | Plotting several genes | Splitting plots by groups | Shared scales and legends | Nested group plots | Palettes | Categorical palettes and Named categorical palettes | Rasterizing dense point layers | Saving plots | Session information
Package: scOverlay 0.99.0
Bernat Gel
scOverlay: Multilayer plots for single-cell data
scOverlay provides publication-grade plotting helpers to display a foreground feature (gene expression or metadata) on top of a contextual background (clusters, cell types, samples, or a solid colour) in the same reduced dimension panel, each with independent colour scales (via ggnewscale). It integrates with SingleCellExperiment / SummarizedExperiment, supports flexible subsetting of foreground cells, multiple assays (e.g. counts, logcounts), and grid arrangements by user-defined grouping columns.
Authors:
scOverlay_0.99.0.tar.gz
scOverlay_0.99.0.zip(r-4.7-any)scOverlay_0.99.0.zip(r-4.6-any)scOverlay_0.99.0.zip(r-4.5-any)
scOverlay_0.99.0.tgz(r-4.6-any)scOverlay_0.99.0.tgz(r-4.5-any)
scOverlay_0.99.0.tar.gz(r-4.7-any)scOverlay_0.99.0.tar.gz(r-4.6-any)
scOverlay_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
scOverlay/json (API)
| # Install 'scOverlay' in R: |
| install.packages('scOverlay', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bernatgel/scoverlay/issues
Datasets:
- sce_mpnst_example - Example MPNST SingleCellExperiment for the scOverlay vignette
- sce_overlay_example - Small example SingleCellExperiment for scOverlay
softwarevisualizationsinglecelltranscriptomicsgeneexpressiondatarepresentation
Last updated from:a1e68884d4. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 170 | ||
| linux-devel | NOTE | 315 | ||
| source / vignettes | OK | 339 | ||
| linux-release | NOTE | 297 | ||
| macos-release | NOTE | 256 | ||
| macos-oldrel | NOTE | 242 | ||
| windows-devel | NOTE | 245 | ||
| windows-release | NOTE | 245 | ||
| windows-oldrel | NOTE | 173 | ||
| wasm-release | OK | 117 |
Exports:getPalettelistPalettesplotGeneOverlayplotOverlayplotOverlayPerGroupplotOverlayPerNestedGroup
Dependencies:abindbase64encbeeswarmBiobaseBiocGenericsCairoclicpp11DelayedArrayfarvergenericsGenomicRangesggbeeswarmggnewscaleggplot2ggrastrgluegtableIRangesisobandjsonlitelabelinglatticelifecycleMatrixMatrixGenericsmatrixStatspatchworkpngR6raggRColorBrewerrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraystringiSummarizedExperimentsystemfontstextshapingvctrsviporviridisLitewithrXVector
scOverlay: layered visualization of single-cell embeddings
Last update: 2026-06-02
Started: 2026-06-02
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Resolve a scOverlay palette | getPalette |
| List available scOverlay palettes | listPalettes |
| Plot overlays for several genes | plotGeneOverlay |
| Plot layered information on a single-cell embedding | plotOverlay |
| Plot overlays split by a cell metadata group | plotOverlayPerGroup |
| Plot overlays arranged by nested cell metadata groups | plotOverlayPerNestedGroup |
| Example MPNST SingleCellExperiment for the scOverlay vignette | sce_mpnst_example |
| Small example SingleCellExperiment for scOverlay | sce_overlay_example |