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. 2023 Mar 2;23:199. doi: 10.1186/s12885-023-10675-y

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© The Author(s) 2023

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. 4 — Pseudotime trajectory reconstruction of macrophage reprogramming course. a,b Pseudotime trajectory was reconstructed on the whole macrophage compartment containing one branch point. Cells of different States are denoted with different colors (left panel). Cells are highlighted according to the pseudotime ranging from 0 to 20 (right panel). c Each macrophage subset (left panel) and whole macrophage subsets (right panel) were projected onto the trajectory plots with different colors assignment. d Heatmap presents a differentially expressed genes by comparing two cell states (q < 10^− 50), each row represents expression level of each gene along the branch trajectory. e Pseudotime kinetics of representative genes from the root of the trajectory to cell fate 1 (solid line) or cell fate 2 (dashed line), with each dot representing a single cell and color-coded by cell identity