Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2021 Jan 4;22:10. doi: 10.1186/s13059-020-02238-2

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2021

Open AccessThis 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.

PMC Copyright notice

Fig. 3 — scMC aligns and preserves condition-specific cell subpopulations on perturbed PBMC datasets. a UMAP of the corrected data from LIGER, Seurat V3, Harmony, and scMC across control and stimulated conditions in the perturbed PBMC datasets. Each row represents one method, and each column represents one perturbed dataset in which only one cell subpopulation was retained in the control condition (indicated on the top). See Additional file 2: Figure S3A for other 7 perturbed datasets. Green: cells retained in the control condition; blue: cells from the corresponding same cell subpopulation in the stimulated condition; gray: other cells in the stimulated condition. b LISI-derived F1 scores of LIGER, Seurat V3, Harmony, and scMC on all 13 perturbed datasets. c UMAP of the corrected data from LIGER, Seurat V3, Harmony, and scMC across control and stimulated conditions. Each column represents one perturbed dataset, where the cell subpopulation removed in the control condition is labeled on the top, and CD14 Mono and DC cell subpopulations were also removed in the stimulated condition for all cases. See Additional file 2: Figure S3B for other 7 perturbed datasets. Green: CD14 Mono and DC cells from the control condition. Red: other cells from the control condition. Blue: cells of the cell subpopulation removed from the control condition in the stimulated condition. Purple: other cells in the stimulated condition. d Specificity scores of LIGER, Seurat V3, Harmony, and scMC on all 13 perturbed datasets