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. 2020 Apr 14;11:1801. doi: 10.1038/s41467-020-15543-y

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© The Author(s) 2020

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 Th0-stimulated T_N and T_M cells ordered in a branched pseudotime trajectory. Cells are colored by cell type (top panel) or effectorness (bottom panel). b Heatmap of the most variable genes along the Th0 pseudotime trajectory (Methods). The x axis represents cells ordered by effectorness (from left to right) and colors correspond to the scaled (Z-scored) expression of each gene in each cell. c Mapping of Th0-stimulated cells to their corresponding resting T cell populations. Integration of resting and Th0-stimulated cells using canonical correlation analysis (Methods) followed by UMAP embedding. Cells are colored by activation status (resting vs Th0, top panel) or cell type (bottom panel). d Density plots highlighting the location of cell clusters as defined in resting state. e UMAP embedding color-coded by the effectorness values of resting and stimulated cells. Source data are provided as a Source Data file.