reglScatterplotR

reglScatterplotR is an htmlwidgets interface to the JavaScript regl-scatterplot library, rendering millions of two-dimensional points in the browser via WebGL. Built for exploratory visualisation of single-cell, spatial transcriptomics and other high-dimensional biological data.

Features

• WebGL-accelerated point rendering — 5M points smoothly, 10M+ usable.
• Categorical and continuous colour mapping with RColorBrewer / viridisLite palettes.
• Draggable legend with click-to-filter, shift / ctrl / cmd extending.
• Lasso selection and synchronised pan/zoom across multiple widgets.
• PNG / SVG / PDF export.
• Shiny output / render bindings + custom-message handlers for live updates.
• Native SingleCellExperiment / SpatialExperiment dispatch.
• Works in the RStudio Viewer, Shiny apps, standalone HTML and Jupyter notebooks running IRkernel.

Installation

# From GitHub (development version)
remotes::install_github("george123ya/reglScatterplotR")

# Once accepted into Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("reglScatterplotR")

Quick start

library(reglScatterplotR)

# Plain data.frame
set.seed(1L)
df <- data.frame(
    x       = rnorm(20000),
    y       = rnorm(20000),
    cluster = sample(letters[1:6], 20000, replace = TRUE),
    score   = runif(20000)
)
reglScatterplot(df, x = "x", y = "y", colorBy = "cluster")
reglScatterplot(df, x = "x", y = "y", colorBy = "score",
                continuousPalette = "magma",
                vmin = "p1", vmax = "p99")

SingleCellExperiment one-liner

library(SingleCellExperiment)
# sce already has reducedDim(sce, "UMAP") + colData(sce)$cluster
reglScatterplot(sce, x = "UMAP", colorBy = "cluster")

# Or colour by a gene
reglScatterplot(sce, x = "UMAP", colorBy = "MS4A1")

SpatialExperiment tissue map

library(SpatialExperiment)
reglScatterplot(spe, x = "spatial", colorBy = "celltype",
                autoFit = TRUE)

Documentation

Topic	Where
Tour with examples	vignette("reglScatterplot")
Scaling to millions of points	vignette("performance")
Wiki: extended recipes	https://github.com/george123ya/reglScatterplotR/wiki
Issue tracker	https://github.com/george123ya/reglScatterplotR/issues

Performance at a glance

Point count	Status	HTML size (typical)
≤ 500 k	Flawless	< 5 MB
500 k – 5 M	Smooth	10 – 40 MB
5 M – 20 M	Usable	50 – 100 MB
> 20 M	Tile architecture territory	—

The widget uses Uint16-quantised binary transfer, so a 1 M-point single-cell UMAP normally fits in a < 10 MB HTML file that you can email or commit.

Citation

citation("reglScatterplotR")

Please also cite the underlying JavaScript library: Lekschas, F. (2023). regl-scatterplot: A WebGL-Powered Scatter Plot Renderer. https://github.com/flekschas/regl-scatterplot

Licence

MIT. See LICENSE.