Fig. 7

Structure in mouse epithelial airway data (n = 7193 cells [86]) inferred from topic modeling (A, B), and GoM DE analysis (D) of selected topics using the membership proportions matrix L shown in A. In C, the topics are annotated by selected distinctive genes (numbers in parentheses are posterior mean l.e. LFCs) and selected enriched gene sets (numbers in parentheses are posterior mean estimates of the enrichment coefficients). In A, to better visualize the rare cell types, the cells were divided into two groups, “abundant” and “rare,” based on the estimated membership proportions, then the “abundant” cells were subsampled. The Structure plot in B was obtained by fitting another topic model, with K = 5 topics, to rare epithelial cell types (defined as the subset of 637 cells i with at least 10% membership to topic 6). The volcano plots show posterior estimates of l.e. LFC vs. posterior z-scores for 18,388 genes. A small number of genes with extreme posterior z-scores are shown with smaller posterior z-scores so that they fit within the y-axis range. See also the interactive volcano plots (Additional file 5: S6), GoM DE results (Additional file 2: Table S2, Additional file 1: Figs. S6; S7), and GSEA results (Additional file 3: Tables S5, S6)