Hi I am still relatively new to scanpy. I am having trouble understanding the sc.pl.dotplot output.
When I read in my h5ad file and check if a gene is present, it yields false:
adata = sc.read(file.h5ad) 'CEACAM8' in adata.var_names.to_list() False
But later when I try and plot the gene the result is a dotplot showing expression
sc.pl.dotplot(adata, 'CEACAM8', groupby='organ', dendrogram=False, title='CEACAM8 expression', swap_axes = True, use_raw=True)
I am a bit confused as to what is going on here. If the gene of interest isn’t in var_names, why am I getting a dotplot?