Fig. 6

Reconstruction of a trajectory with Macrophage Subpopulation. a The single-cell trajectory reconstructed by Monocle contains five main branches and two decision points. Cells are colored based on pseudotime (upper) and sample types. Abbreviation: Con, MO, SE indicate Control, Moderate, and Severe, respectively. b Dot plot showing the variability of gene expressions, such as C1QA (upper), CXCL2 (middle), and TREM2, following pseudotime based on cell states. A natural spline was used to model gene expression as a smooth, nonlinear function over pseudotime. c Dot plot showing the variability of pathway activity, such as hypoxia (upper), glycolysis (middle), and senescence, following pseudotime in the path that contains cells of states 1, 2, 3, 4, and 5. d, e Each heatmap presents genes differentially expressed between two branch comparisons, and each row represents the expression level of a gene along the branch trajectory. Enriched pathways are summarized for each gene cluster. From root to state 1 and state 2 branches (d), from root to state 2, and combined state 3 with 4 branches (e)