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. 2021 May 17;22:157. doi: 10.1186/s13059-021-02368-1

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© The Author(s) 2021

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 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. 6 — Results of comparing cortex tissue from vehicle and LPS-treated mice at different resolution levels of cell types. a A tree encodes information of cell subpopulations at different resolutions. The cell numbers for each subpopulation are given for each leaf. The median expression of 13 canonical type markers, each columnwise scaled to [0,1], is shown in the left heatmap. The identified DS genes are shown in the right heatmap (each column is a gene, each row subpopulation; upregulated in the LPS group in orange, downregulated in blue). b Volcano plots (-log P value versus log fold change) with the 30 genes with highest absolute logFC colored in red. Number of down- and upregulated genes are labelled on the left and right side of the dashed line at logFC=0. c Heatmaps of top 30 genes (red points in b, ordered by decreasing logFC