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. 2022 Oct 28;5:1142. doi: 10.1038/s42003-022-04093-2

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© The Author(s) 2022

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. 3 — a Schematic of specificity-based resolution-selection criteria. b, c Adjusted Rand index (b) and specificity index differences (c) between ground truth (author-curated) clusters and observed Louvain clusters, using resolutions determined by different optimization criteria [specificity criteria ( $S_{p e a k}, S_{e l b o w 1}, S_{e l b o w 2}$ ) and chooseR⁵⁸]. $A R I_{\max}$ represents resolution at which maximal ARI was achieved, after considering all candidate resolutions (0.5–3). For b, significance compared to ARI_maxdetermined by paired Wilcoxon test. For c, significance compared to zero (i.e., ground truth) was determined by one-sample Wilcoxon test. N = 8 independent scRNA-seq datasets. d–g Optimal clustering resolution for Tyser 2021 human gastrulation scRNA-seq data¹⁷. d Relationship between resolution and specificity indices, and identification of $S_{p e a k}$ , $S_{e l b o w 1}$ and $S_{e l b o w 2}$ . e Specificity-curves. Gray curves: all candidate resolutions evaluated (0.5–3), blue curve: S_peak, red curve: ground truth (curated) clusters. f Dot plots of top markers for curated (left) and $S_{p e a k}$ (right) clusters. g Comparison of cluster sensitivity (expressing fraction) of each top marker obtained for curated and $S_{p e a k}$ clusters. Significance determined by unpaired Wilcoxon test.