Fig. 2

A hierarchy of mammalian cell types from single-cell transcriptomes. a, b Recovery of individual reference cell types by HiDeF (y axis) in comparison to Conos [19] or TooManyCells [18] (x axis of a or b, respectively). For each reference cell type (points), the extent of recovery is measured as the maximum F1-score of the set of reference cells with those of any detected community (see the “Methods” section). c Recovery of reference cell types (evaluated by the average F1-score) among the top N ranked cell communities. Communities are ranked in the descending order of score for each community detection tool (e.g., persistence in HiDeF; see the “Methods” section). d Hierarchy of 273 putative mouse cell types identified by HiDeF. Vertices are cell communities, with color gradient indicating the extent of the optimal match (Jaccard similarity) to a reference cell type. Selected matches to reference cell types are labeled. Gray regions indicate sub-hierarchies (epidermal cells, astrocytes/neurons, and hepatocytes) related to subsequent panels and other figures (Additional file 1: Figure S4). e Epidermal cell communities. Left: UMAP 2D projection of all cells, with epidermal cells highlighted in dark blue. Middle: sub-hierarchy of epidermal cell communities as determined by HiDeF. Right: correspondence between the UMAP projection and the sub-hierarchy, with colors marking the same cell populations across the two representations. f Astrocyte and neuron communities. Left: UMAP 2D projection of all cells, with astrocytes and neurons highlighted in dark blue. Middle: sub-hierarchy of astrocyte and neuron communities as determined by HiDeF. Cells in the three small communities are highlighted in the below UMAP projections. Right: broader UMAP context with cells colored and labeled as per the original Tabula Muris analysis [16]. Results in this figure are based on the FACS dataset in the Tabula Muris [16]; similar results were obtained for the Tabula Muris droplet dataset (Additional file 1: Figure S3)