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. 2021 Oct 14;12:6012. doi: 10.1038/s41467-021-26271-2

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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. 2 — A Morphological regions were annotated by a pathologist into six distinct categories: adipose tissue (cyan), breast glands (green), in situ cancer (orange), connective tissue (blue), immune infiltrate (yellow), and invasive cancer (red). B Split view of each expression-based cluster’s distribution across one tissue section. C UMAP embedding of all spots (n = 446) from the three replicates, markers are colored based on cluster identity. D Proportions of spots assigned to each cluster across the three replicates. E Dot plot showing the overlap between clusters and annotated regions. The size of the dots represents the proportion of cluster spots belonging to an annotated region. The pathologist’s annotations are given on the x axis, cluster annotations on the y axis. F. Heatmap of the clusters and the most highly differentially expressed genes. Each cluster was annotated based on its association with morphological regions and marker genes. Heatmap colors represent normalized and scaled expression values. APC stands for antigen-presenting cell.