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. 2023 Sep 12;14:5618. doi: 10.1038/s41467-023-41437-w

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© The Author(s) 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 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/.

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Fig. 3 — a UMAP visualizations of raw data and the enhanced data of the nontumor cell population. b Violin plots of the raw expression and the enhanced expression of marker genes in different cell populations (endothelial: 4272; epithelial: 3458; fibroblast: 13,368; lymphocyte: 11,664; mast: 287; M-cell: 7560; neutrophil: 5731; tumors: 37,281). c UMAP visualization of the raw expression and the enhanced expression of marker genes (CD68, MGP, DCN, KRT7). d Spatial visualization of the raw expression and the enhanced expression of tumour-related genes (EPCAM, KRT7, SOX4) in two FOVs. e Scatter plot of significantly associated ligand‒receptor (L-R) pairs in the raw data and the enhanced data. Orange- and yellow-coloured dots represent the shared and specific L-R pairs, respectively. Source data are provided as a Source Data file. f Network representation of the weighted adjacent cell types. The edge width represents the adjacency between two cell types. g Adjacent cell communications considering both neighbouring cell weights and L-R interaction strength.