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. 2021 Dec 15;22:341. doi: 10.1186/s13059-021-02546-1

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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 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 3 — Examples of complex splatPop simulations. A principal component analysis (PCA; top) plot of the simulations with each individual designated by color and each complex effect denoted by shape and the distribution of the degree of variance in gene expression across cells explained by the experimental factor (bottom) for simulations with a batch effects using ss2-iPSC as a reference, b cell group effects using 10x-Neuro as a reference, and c conditional effects using 10x-IPF as a reference. Note, no variance in gene expression is explained by individual using the 10x-Neuro reference