scOverlay: Multilayer plots for single-cell data

Description

scOverlay creates layered visualizations of single-cell data stored in SingleCellExperiment objects. It is designed to show one layer of information as context, such as clusters, samples or gene expression, while overlaying a second layer of information on top of it.

The package is especially useful to highlight subsets of cells, gene expression, metadata annotations or quality-control scores while preserving the global structure of a t-SNE, UMAP or other reduced-dimension representation.

Installation

scOverlay is a Bioconductor package (in process). Once available from Bioconductor, it can be installed with:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("scOverlay")

The development version can be installed from GitHub with:

if (!requireNamespace("remotes", quietly = TRUE)) {
    install.packages("remotes")
}

remotes::install_github("bernatgel/scOverlay")

Getting started

library(scOverlay)

data("sce_overlay_example")

plotOverlay(
    sce = sce_overlay_example,
    foreground = "CDH19",
    background = "cluster",
    reduced_dim = "TSNE"
)

background and foreground can be a gene, a cell annotation from colData(sce), "solid" or "none".

plotOverlay(
    sce = sce_overlay_example,
    foreground = "scDblFinder.score",
    background = "cluster",
    fg_subset_cells = quote(cluster == "1"),
    fg_palette = "red",
    reduced_dim = "TSNE"
)

Grouped plots can be created with plotOverlayPerGroup():

plotOverlayPerGroup(
    sce = sce_overlay_example,
    group_col = "sample_type",
    foreground = "PRRX1",
    background = "cluster",
    reduced_dim = "TSNE",
    fg_limits = "shared",
    shared_legend = TRUE
)

Documentation

The package vignette provides a more complete introduction to the layered plotting model, palettes, foreground subsetting, grouped plots, rasterization and saving figures.

• Bioconductor landing page: https://bioconductor.org/packages/scOverlay
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/scOverlay/inst/doc/scOverlay.html
• Development repository: https://github.com/bernatgel/scOverlay

Bioconductor links will become active once the package is available from Bioconductor.

Main features

• Layered visualization of single-cell embeddings.
• Support for gene expression and cell metadata in both background and foreground layers.
• Foreground subsetting without removing the full embedding context.
• Grouped and nested grouped plots.
• Shared scales and shared legends for grouped visualizations.
• Named categorical palettes for consistent colours across panels.
• Optional rasterization of dense point layers.
• Standard ggplot2 output objects that can be further customized.

Citation

If you use scOverlay in published work, please cite it with:

citation("scOverlay")

A formal citation will be added once available.

License

scOverlay is distributed under the Artistic-2.0 license.

Bug reports and feature requests

Please use the GitHub issue tracker to report bugs or request features:

https://github.com/bernatgel/scOverlay/issues