Dimensionality reduction for visualizing single-cell data using UMAP

• Published in: Nature biotechnology Vol. 37; no. 1; pp. 38 - 44
• Main Authors: Becht, Etienne, McInnes, Leland, Healy, John, Dutertre, Charles-Antoine, Kwok, Immanuel W H, Ng, Lai Guan, Ginhoux, Florent, Newell, Evan W
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.01.2019; Nature Publishing Group
• Subjects: 631/114; 631/114/2164; 631/250; Agriculture; analysis; Approximation; B cells; Bioinformatics; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Bone marrow; Cells (Biology); Cytometry; Datasets; Dendritic cells; Flow cytometry; Gene sequencing; Life Sciences; Lymphocytes; Medical research; Principal components analysis; Reduction; Reproducibility; Ribonucleic acid; RNA; RNA sequencing; Surgery; Transcription (Genetics); Visualization (Computer)
• ISSN: 1087-0156; 1546-1696; 1546-1696
• DOI: 10.1038/nbt.4314

A benchmarking analysis on single-cell RNA-seq and mass cytometry data reveals the best-performing technique for dimensionality reduction. Advances in single-cell technologies have enabled high-resolution dissection of tissue composition. Several tools for dimensionality reduction are available to analyze the large number of parameters generated in single-cell studies. Recently, a nonlinear dimensionality-reduction technique, uniform manifold approximation and projection (UMAP), was developed for the analysis of any type of high-dimensional data. Here we apply it to biological data, using three well-characterized mass cytometry and single-cell RNA sequencing datasets. Comparing the performance of UMAP with five other tools, we find that UMAP provides the fastest run times, highest reproducibility and the most meaningful organization of cell clusters. The work highlights the use of UMAP for improved visualization and interpretation of single-cell data.