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. 2023 Jan 18;14:296. doi: 10.1038/s41467-023-35947-w

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© The Author(s) 2023, corrected publication 2023

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. 5 — a Top panel: H& E images from four tissue slides. Bottom panel: Manual annotation by a pathologist of four tissue slides. b Top panel: UMAP RGB plots of PRECAST for four tissue slides. Bottom panel: Clustering assignment heatmaps for four tissue sections by PRECAST. Color scheme for clustering assignment heatmap in PRECAST is the same as in (c), (f), and (g). c tSNE plots for four data integration methods with the right-most column showing analysis without correction; domains are labeled as in (e) and (f). TNE, tumor/normal epithelium. d Spatial heatmap of deconvoluted cell proportions in malignant cells, immune cells, and HPC-like cells. e Percentage of different cell types in each domain detected by PRECAST, with scaling to the summation of all cell types across all domains equal to 100%. f PC plot of estimated RNA velocity. g Heatmap of genes with expression change in latent time.