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. 2021 May 5;12:2540. doi: 10.1038/s41467-021-22801-0

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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 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. 4 — a UMAP visualization of 6 T cell subtypes and 2 NK cell subtypes (left) and predicted T cell subtypes by singleR (right). b Heatmap of selected markers for 2 NK clusters. c Heatmap of T subtype markers and selected functional genes. d Transitional relationship among CD4 T cells predicted by Slingshot. Rainbow coloring from red to blue represented the begin to end of the trajectory. e Illustration of CD4 T cell differentiation pathways inferred by Monocle and the relative locations of each CD4 T subtypes along the development pathways. The red and blue arrows indicated the two pseudotime directions of cell development. The grey section represented the beginning of the trajectory before the branching point. f Heatmap showing relative expressions of canonical markers of CD4 T cells along inferred trajectories. The red and blue branches correspond to the two developmental directions in e.