scOverlay
This is the development version of scOverlay; to use it, please install the devel version of Bioconductor.
Multilayer Plots for Single-Cell Data
Bioconductor version: Development (3.24)
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.
Maintainer: Bernat Gel <bgel at igtp.cat>
citation("scOverlay")):Bernat Gel. scOverlay: Multilayer Plots for Single-Cell Data. doi:10.18129/B9.bioc.scOverlay, R package version 0.99.5, https://bioconductor.org/packages/scOverlay.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scOverlay")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scOverlay")| scOverlay: layered visualization of single-cell embeddings | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, GeneExpression, SingleCell, Software, Transcriptomics, Visualization |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | ggplot2, ggnewscale, SummarizedExperiment, SingleCellExperiment, viridisLite, scales, RColorBrewer, patchwork, ggrastr, rlang |
| System Requirements | |
| URL | https://github.com/bernatgel/scOverlay |
| Bug Reports | https://github.com/bernatgel/scOverlay/issues |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scOverlay_0.99.5.tar.gz |
| Windows Binary (x86_64) | scOverlay_0.99.5.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | scOverlay_0.99.5.tgz |
| macOS Binary (sonoma-arm64) | scOverlay_0.99.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scOverlay |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scOverlay |
| Package Short Url | https://bioconductor.org/packages/scOverlay/ |
| Package Downloads Report | Download Stats |