FIGURE 4.

Lineage convergence and two-way conversion of fibroblasts in lung regeneration. a, d, g) CellRank's coarse-grained and directed transition matrix was calculated for the given three phases of the bleomycin lung injury time course, of early phase (day 2 to day 5), fibrogenesis phase (day 6 to day 21) and resolution phase (day 28 to day 54). Terminal macrostates were set manually and annotated according to their overlap with the underlying gene expression clusters. The heatmap represents the mean absorption probabilities of every cell in the given cell types to the terminal fates. b, e, h) Violin plots indicating the absorption probability towards the specified fate for every cell in all the cell types. c, f, i) Scatter plots show top driver genes, predicted to facilitate transition to the given terminal fate, visualised as gene-correlations between two terminal fate lineages. The top genes of a third lineage are visible by the third colour of the gene names. Dots are coloured according to their mean gene expression. SMC: smooth muscle cell.