[SOLVED] subsetting anndata on basis of louvain clusters

subsetting anndata on basis of louvain clusters

I want to subset anndata on basis of clusters, but i am not able to understand how to do it.

I am running scVelo pipeline, and in that i ran tl.louvain function to cluster cells on basis of louvain. I got around 32 clusters, of which cluster 2 and 4 is of my interest, and i have to run the pipeline further on these clusters only. (Initially i had the loom file which i read in scVelo, so i have now the anndata.)

I tried using adata.obs["louvain"] which gave me the cluster information, but i need to write a new anndata with only 2 clusters and process further.

Please help on how to subset anndata. Any help is highly appreciated. (Being very new to it, i am finding it difficult to get)

Solution

If your adata.obs has a "louvain" column that I'd expect after running tl.louvain, you could do the subsetting as adata[adata.obs["louvain"] == "2"] if you want to obtain one cluster and adata[adata.obs['louvain'].isin(['2', '4'])] for obtaining cluster 2 & 4.