How the clusters are identified?

[huizizhang949]

Hi,

I have a dataset with 10 defined clusters in the beginning. But after running the dynamic model and velocity estimation, the velocity embedding shows 12 clusters. Is there any step in the middle to identify clusters? How?

Thank you!

[WeilerP]

No, there isn't. My best guess/suggestion is to check that you are coloring the embedding according to the correct column in adata.obs, i.e., the color argument is set correctly.

[huizizhang949]

Thank you! I notice that my embedding 'title' is louvain which seems to be new column of labels added to the data. Are they clusters? How can I add my clusters 'adata.obs.Clusters' as labels?

[WeilerP]

You must have run Louvain clustering at some point. To color the embedding by according to the column 'Clusters', you need to pass color='Clusters'. Please have a look at the docs.