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. 2023 May 25;42(2):284–292. doi: 10.1038/s41587-023-01766-z

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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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Extended Data Fig. 2 — a. Number of 10X PBMC Multiome cells assigned to each simulated data type (left), joint UMAP generated using StabMap coloured by simulated data type (middle), and by cell type (right). b-j. As in panel (a.) for decreasing proportions of simulated Multiome cells. k. Local inverse Simpson indices (LISI) for simulated data type (top row) and for cell type (bottom row). LISI values are extracted for all integrated cells (n = 10,032). Each boxplot (median bar and whiskers to quartiles) corresponds to different choices of number of cells in the multiome dataset. The dotted line indicates approximately 1,000 cells in the multiome dataset, where LISI values appear to markedly shift from unfavourable to favourable integration. l. Joint UMAP embedding generated using StabMap in simulation as described in Fig. 3, with RNA dataset selected as reference, indicating a ‘multi-hop’ data integration.