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. 2023 Mar 27;10:167. doi: 10.1038/s41597-023-02074-6

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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 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 — Quality of the final dataset. (a) Violin plots showing QC metrics of cells included in the final dataset, including percentage of counts from mitochondrial genes (Percent_mt) and number of genes (nFeature_RNA), split by study. (b) Removal of the batch effect presented by PCA and dimensional reduction plots (c) for the final dataset, in a comparison to a merged dataset without batch correction. (d) Distribution of cells from the seven analyzed datasets in the clusters of the final dataset. (e) UMAP plots of the final dataset cells grouped by clinical metadata, including gender, subtype, stage, and patient.