Fig. 4
Pseudotime trajectory reconstruction of macrophage reprogramming course. a,b Pseudotime trajectory was reconstructed on the whole macrophage compartment containing one branch point. Cells of different States are denoted with different colors (left panel). Cells are highlighted according to the pseudotime ranging from 0 to 20 (right panel). c Each macrophage subset (left panel) and whole macrophage subsets (right panel) were projected onto the trajectory plots with different colors assignment. d Heatmap presents a differentially expressed genes by comparing two cell states (q < 10− 50), each row represents expression level of each gene along the branch trajectory. e Pseudotime kinetics of representative genes from the root of the trajectory to cell fate 1 (solid line) or cell fate 2 (dashed line), with each dot representing a single cell and color-coded by cell identity