The direction of PAGA graph is inconsistent with the stream plot

[shexiaolu]

Hi! Thanks for your tool! I want to ask why there is different direction between PAGA graph and stream plot?It is really confused me


I will be looking forward to your reply!Thanks!

[zhanglab2008]

@shexiaolu I likes the way you overlay the PAGA trajectory and umap plot. Could you show me a way to do this?
Thanks!

[WeilerP]

@VolkerBergen any idea what's causing this and how to potentially fix it?

[VolkerBergen]

That's strange indeed. Could be caused by very low signal, yet a complete direction reversal is bit suspicious.

Could you run a couple cell transition from some of the presumed root cells, as shown in ln 20 here?

[WeilerP]

@enigmaticsloth, could you please provide the stream plot, PAGA graph and top likelihood genes?

[hyjforesight]

Hello @shexiaolu, i have the same issue. could you please tell me whether you fixed it? Thanks!

[kxxxjo]

Hi @WeilerP , I haver the same issue. I want to fix this issue, could you let me know how to solve this?

Thanks!

Best,
Kyungjo

[france-hub]

Hello,
Was this solved? I have the same issue.

Thanks
Francesco

[m-rossello]

Hi! I'm experiencing the same issue. Has anyone found a solution? I'm calculating velocities using mode="dynamical". Any advice would be appreciated!