Subsetting anndata on basis of louvain clusters
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14 months ago

Hello, 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)

python scanpy anndata R RNA-Seq • 1.6k views
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Entering edit mode
9 months ago

adata = adata[adata.obs['louvain'].isin(['2','4'])]

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