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. 2021 Dec 6;22:333. doi: 10.1186/s13059-021-02548-z

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© The Author(s) 2021

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — geneBasis preserves local and global structure. Each column represents the results for a different biological system. A Co-expression within top 10 selected by geneBasis genes. B Upper panel: The overall convergence of cell neighborhood preservation distributions for geneBasis (in red) and SCMER (in blue) as a function of the number of selected genes. Lower panel: the weight of tails of the distributions (i.e., fraction of cells with neighborhood preservation score < 0.5). Values are rescaled as ln(x + 1). C The fraction of cells mapped to the correct cell type for geneBasis (in red) and scGeneFit (in orange) as a function of number of genes in the selection. D Upper panel: The distribution of neighborhood preservation scores (calculated for the first 150 genes) per cell type. Lower panel: UMAP representation colored by neighborhood preservation score (calculated for the first 150 genes). UMAP coordinates themselves were calculated using the whole transcriptome. For visualization purposes, cell neighborhood preservation scores lower than 0 were set equal to 0