Scanpy Ingest Understanding

I am using the following code to run my ingest function…

control_results = ‘pathway’
nicotine_results = ‘pathway’
adata_ctrl =
adata_nicotine =

confirmed ctrl is condition 1 and confirmed nicotine is condition 2 via adata.obs

shared_genes = adata_nicotine.var_names.intersection(adata_ctrl.var_names)
adata_ctrl_ing = adata_ctrl[:, shared_genes].copy()
adata_nicotine_ing = adata_nicotine[:, shared_genes].copy()

adata_mapped =, adata_ctrl_ing, obs=‘leiden’, inplace=False)

Now at this point when I run adata_mapped.obs I notice that condition 2 is only present i.e. my non reference group? My understanding of Ingest was that I would have option A) condition 1 and 2 in a new adata_mapped that I could then make comparisons between and the nicotine clustering would be based on my saline data set. But for some reason it looks like my adata_mapped is actually option B) my nicotine set clustered using my saline as reference but my saline is no longer part of this data set. Can someone explain which of my understandings option A or B is correct?