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

. 2023 Jun 8;29(6):1563–1577. doi: 10.1038/s41591-023-02327-2

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

© 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/.

PMC Copyright notice

Fig. 2 — a, Donor and sample composition in the HLCA core for demographic and anatomical variables. Donors/samples without annotation are shown as not available (NA; gray bars) for each variable. For the anatomical region CCF score, 0 represents the most proximal part of the lung and airways (nose) and 1 represents the most distal (distal parenchyma). Donors show diversity in ethnicity (harmonized metadata proportions: 65% European, 14% African, 2% admixed American, 2% mixed, 2% Asian, 0.4% Pacific Islander and 14% unannotated; see Methods), smoking status (52% never, 16% former, 15% active and 17% NA), sex (60% male and 40% female), age (ranging from 10–76 years) and BMI (20–49; 30% NA). b, Overview of the HLCA core cell type composition for the first three levels of cell annotation, based on harmonized original labels. In the cell type hierarchy, the lowest level (1) consists of the coarsest possible annotations (that is, epithelial (48% of cells), immune (38%), endothelial (9%) and stromal (4%)). Higher levels (2–5) recursively break up coarser-level labels into finer ones (Methods). Cells were set to ‘none’ if no cell type label was available at the level. Cell labels making up less than 0.02% of all cells are not shown. Overall, 94, 66 and 7% of cells were annotated at levels 3, 4 and 5, respectively. c, Cell type composition per sample, based on level 2 labels. Samples are ordered by anatomical region CCF score. d, Summary of the dataset integration benchmarking results. Batch correction score and biological conservation score each show the mean across metrics of that type, as shown in Supplementary Fig. 1, with metric scores scaled to range from 0 to 1. Both Scanorama and fastMNN were benchmarked on two distinct outputs: the integrated gene expression matrix and integrated embedding (see output). The methods are ordered by overall score. For each method, the results are shown only for their best-performing data preprocessing. Methods marked with an asterisk use coarse cell type labels as input. Preprocessing is specified under HVG (that is, whether or not genes were subsetted to the 2,000 (HVG) or 6,000 (FULL) most highly variable genes before integration) and scaling (whether genes were left unscaled or scaled to have a mean of 0 and a standard deviation of 1 across all cells). EC, endothelial cell; NK, natural killer; Bioconserv., conservation of biological signal.