Extended Data Fig. 3: Multiscale PHATE is capable of identify extractable cellular subsets from massive single-cell data.

a, Multiscale PHATE visualization of PBMCs identifies all major cell types based on cell type–specific markers. b, PHATE visualization of subsample of 25,000 PBMCs helps identify all major cell types based on cell type–specific markers using Multiscale PHATE clustering. c, Zoom in of subsection of Multiscale PHATE manifold resolves crowding in coarse grain visualization. d, Zoom in of subsection of PHATE manifold does not resolve crowding. e, Multiscale PHATE is able to identify subpopulations enriched in patients who die from COVID. The plot on the right is colored by Multiscale PHATE-identified clusters. f, PHATE and vertex frequency clustering (VFC) are unable to identify subpopulations enriched in patients who die from COVID. The plot on the right is colored by VFC identified clusters. g, Multiscale PHATE-identified populations show differing enrichments in patients who die from COVID19. One of the B cell subsets (lighter blue color) are enriched in patients who die from COVID. h, Multiscale PHATE’s hierarchical approach to clustering provides a gating strategy to isolate subsets of B cells enriched in patients who die from COVID19. i, VFC identified populations do not isolate mortality enriched cellular subsets as well as Multiscale PHATE.