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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 (>= 4.6.0) |
| 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 |
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) | |
| macOS Binary (big-sur-x86_64) | scOverlay_0.99.5.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/scOverlay |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scOverlay |
| Bioc Package Browser | https://code.bioconductor.org/browse/scOverlay/ |
| Package Short Url | https://bioconductor.org/packages/scOverlay/ |
| Package Downloads Report | Download Stats |