Calculate cell level plasticity score

[YushaLiu]

Hi Matt, I saw from the KPTracer repository that Fitch-Hartigan maximum parsimony can now be calculated in Cassiopeia. Can I calculate the cell-level "scEffectivePlasticity" score in Yang et al. using Cassiopeia, or only the tree-level "EffectivePlasticity" score? Thanks very much!

Yusha

[mattjones315]

Hi @YushaLiu,

Thanks for your question! Yes, this is possible with the current Cassiopeia codebase - please see the section entitled "Inferring tree plasticity" from our tutorial in Single-Cell Best Practices.

Best of luck and please let me know if I can be of any further assistance.

Best, Matt

[YushaLiu]

Great, thanks so much for your quick reply!

[YushaLiu]

Hi @mattjones315, I have a quick follow-up question on this. For fast expanding clades that contain polytomies, that is, a large number of cells whose phylogenetic relationships cannot be further resolved because they share the same mutation patterns (e.g., the magenta region in the upper right and the light sky blue region in the lower right part of the tree I attached), how did you assess the plasticity level of such cells in Yang et al., which also seems to have the same problem in some tumors (e.g., 3433_NT_T2 in Fig. 4B, 3513_NT_T3 in Fig. 5C)? And further, if I want to compare the plasticity level of the fast expanding clades (cells highlighted in color in the inner circle) to the non-expanding clades (cells in black in the inner circle), is there a way to do that? In the attached plot, the color from the outer circle represents the harvest sites or transcriptional states of cells. Thanks very much!