I am using scanpy to cluster and label my scRNA seq data. I have several genes of interest and would like to identify from which cluster they are expressed from. When I run:
adata.var[adata.var_names == 'LINC01138:23']
I get a table with the gene id, n_cells_by_counts and total_counts amongst other columns. In the total_counts, there are 82 cells that express the LINC01138:23. I am trying to find out which cells the LINC01138:23 gene is expressed in, but since the cluster data is in adata.obs, I am unsure how to find this data.
The genes I have are not highly expressed, so I cannot find it when I run
markers[markers.names == 'LINC01138:23']
I have tried subsetting my data depending on which clusters I think they belong to, but the total_counts does not change even though I am sure they appear in other clusters than the ones I subsetted. Any help will be appreciated!