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. 2020 Nov 11;11:5702. doi: 10.1038/s41467-020-19542-x

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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. 2 — The mix is composed of human cells from an untreated PDX (HBCx-22), human T cells (Jurkat), and B cells (Ramos) taken from¹ and from a TNBC cell line (MDA-MB-468). (a) UMAP plots obtained with ChromSCape colored according to cluster and sample of origin. Adjusted Random Indexes (ARI) are indicated above the plot. (b) UMAP plots colored according to cluster and sample of origin with other single-cell epigenomic analysis methods: Cusanovich2018, SnapATAC, CisTopic, and EpiScanpy. Adjusted Random Indexes (ARI) are indicated above the plots. (c) Snapshots from scOrange and SCRAT applications. PCA and t-SNE representations from scOrange and SCRAT respectively, using default parameters or after manually optimizing parameters.