How to interpret the PAGA result (sc.pl.paga)

I am a fresh man for the force-directed figure. And I recently plot such figure under the requirement of reviewers. However, I don’t know how to explain the bar and spot in the figure: what’s the meaning of the thickness of the bar connecting two circles; what’s the meaning of the circle size?

Here I post a example figure with 3 cell types, “S”, “G1”, and “G2M”. Could you please explain this figure?

The size of the circles depends on the number of cells in the cluster, and the thickness of the lines represents the strength of the connection. This strength is related to the overrepresentation of edges in the KNN graph between cells in the two clusters. I would suggest you read the PAGA paper to better understand the method and what you are showing: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1663-x

Thank you so much! :smile: