scellop: A Scalable Redesign of Cell Population Plots for Single-Cell Data

Three panels (A-C) with cell population plots. A) Heatmap with bar charts on the top and left and colored legends on the right and bottom. B) Same heatmap as A, but two rows are now bar charts. C) Stacked bar chart with colors for cell types.

Abstract

Summary: Cell population plots are visualizations showing cell population distributions in biological samples with single-cell data, traditionally shown with stacked bar charts. Here, we address issues with this approach, particularly its limited scalability with increasing number of cell types and samples, and present scellop, a novel interactive cell population viewer combining visual encodings optimized for common user tasks in studying populations of cells across samples or conditions. Availability and Implementation: Scellop is available under the MIT licence at https://github.com/hms-dbmi/scellop, and is available on PyPI (https://pypi.org/project/cellpop/) and NPM (https://www.npmjs.com/package/cellpop). A demo is available at https://scellop.netlify.app/.

Citation

TC Smits, N Akhmetov, TS Liaw, MS Keller, E Mörth, N Gehlenborg. “scellop: A Scalable Redesign of Cell Population Plots for Single-Cell Data”, arXiv (2025). doi:10.48550/ARXIV.2510.09554