Seurat Atlas

Interactive visualizations for Seurat single-cell analyses, through Apple's Embedding Atlas.

Overview

seuratAtlas provides an interactive web interface for exploring Seurat objects. The package launches a local web server that displays Seurat embeddings and metadata with real-time querying capabilities and interactions.

Installation

Install the development version from GitHub:

# install.packages("devtools")
devtools::install_github("sanghoonio/seuratAtlas" subdir = "api")

Quick Start

library(Seurat)
library(seuratAtlas)

# process your Seurat object with UMAP
pbmc <- RunUMAP(pbmc, dims = 1:10)

# launch the embedding atlas
seurat_atlas(pbmc)

This will:

1. Start a local web server at http://localhost:3000
2. Automatically open your default browser
3. Display an interactive interface for exploring your data

Features

• Interactive UMAP visualization: Pan, zoom, and select cells
• Real-time querying: Fast SQL-based data filtering with websocket
• Metadata exploration: Query metadata columns with dynamic selections

Documentation

View the package vignette for a detailed tutorial:

vignette("pbmc-tutorial", package = "seuratAtlas")

Building the UI

The UI is prebuilt separately and copied into the package. To rebuild:

cd ../ui
npm run build  # postbuild automatically copies dist folder to api/inst/www/