Fig. 3. Application of CellChat to continuous cell states along pseudotemporal trajectories during embryonic skin development.

a Left: Diffusion map projecting dermal skin cells onto the low-dimensional space and showing the dermal differentiation from fibroblasts to DC (dermal condensate) cells. Cells are grouped based on their location in this space. Right: Density plot showing the distribution of expression for selected marker genes in each cell group/population. b Diffusion map showing the epidermal trajectory and associated density plot for selected marker genes. c Hierarchical plot showing dermal and epidermal interactions via canonical WNT signaling. Left and right portions show the autocrine and paracrine signaling to dermal trajectory and epidermal trajectory, respectively. Circle sizes are proportional to the number of cells in each cell group and edge width represents the communication probability. d Violin plot showing the expression distribution of signaling genes involved in the inferred WNT signaling network. e The dermal and epidermal interactions via ncWNT signaling. f The expression distribution of signaling genes involved in the inferred ncWNT signaling network. g The outgoing signaling patterns of secreting cells visualized by alluvial plot, which shows the correspondence between the inferred latent patterns and cell groups, as well as signaling pathways. The thickness of the flow indicates the contribution of the cell group or signaling pathway to each latent pattern. The height of each pattern is proportional to the number of its associated cell groups or signaling pathways. Outgoing patterns reveal how the sender cells coordinate with each other, as well as how they coordinate with certain signaling pathways to drive communication. h Incoming signaling patterns of target cells. Incoming patterns show how the target cells coordinate with each other, as well as how they coordinate with certain signaling pathways to respond to incoming signaling.