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. 2023 Oct 9;20(11):1683–1692. doi: 10.1038/s41592-023-02035-2

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a,b, Uniform manifold approximation and projections (UMAPs) of Schulte-Schrepping et al. dataset consisting of healthy and COVID-19 PBMC samples after sample-level integration. Cells are colored by cell type (a) and experiment (b), respectively. DC, dendritic cell. NK, natural killer cell. HSPC, hematopoietic stem and progenitor cell. CTL, cytotoxic T cell. TCM, central memory T cell. TEM, effector memory T cell. ILC, innate lymphoid cell. MAIT, mucosal-associated invariant T cell. c–f, Sample embeddings obtained with scPoli colored by experiment (legend shared with b) (c), cohort (d) and disease (e on principal components 1 and 2 and f on principal components 2 and 3). For each covariate the association with the first and second PCs is displayed.