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. 2023 Jan 2;41(6):813–823. doi: 10.1038/s41587-022-01560-3

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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. 1 — Left column: simulation results in a mutually exclusive scenario (that is 1% of loci are overlapping). Middle column: results for an intermediate amount of overlap (that is 50% of loci are overlapping). Right column: results for highly correlated scenario (that is 99% of loci are overlapping). (a) Distribution of unique fragment cuts per cell in simulation. (b) Sparsity of the input matrix. Note that in the mutually exclusive scenario, the double-incubated marks is less sparse than single-incubated marks because loci with zero reads in one mark often have non-zero reads in another mark. (c) Distribution of the degree of overlap (defined as fraction of double-incubated signal belonging to mark1: $p = \frac{S_{1}}{S_{1} + S_{2}}$ ) for each locus genome-wide. (d) Estimated degree of overlap from scChIX-seq. (e) UMAP representation of the three cell types underlying simulation. UMAPs from the two marks are linked by double-incubated cells that are deconvolved by scChIX-seq. (f) Empirical 95% confidence interval across the range of $\hat{p} = \frac{{\hat{S}}_{1}}{{\hat{S}}_{1} + {\hat{S}}_{2}}$ (from 0 to 1). Range obtained by aggregating results from the three overlapping patterns. n=101 simulation datapoints spread evenly between 0 and 1 inclusive. Error bars are empirial 95% confidence intervals, centers are the mean.