Hello,

I’ve been using the cytoTRACE tutorial to visualize pseudo RNA velocity (directed transition matrix). My dataset is composed of time points for 2 conditions and I was wondering if it’s possible to distinguish the contributing directionality per condition, that is, visualize directionality for condition 1 vs condition 2 on the same tsne plot?

Thank you!

Hey @ater153, I guess you could just subset your data, and recompute the k-NN graph on the data subset for visualization.

Hi @Marius1311,

Thank you for your reply, I subsetted the adata taking cells from the 2 conditions. Condition 1 has more cells (2543), condition 2 has 961 cells. All works with adata condition 1 but when I run ctk.compute_transition_matrix(threshold_scheme=“soft”, nu=0.5) for adata condition 2, I get the following error: NetworkXError: Adjacency matrix not square: nx,ny=(961, 960)

Could it be because there needs to be a minimum number of cells?

(If I add cells from naive condition then it works again although graph looks strange).

Thank you so much in advance.