AttributeError after creating SAMAP object

[colinshew]

Hi, I'm having an issue where the SAMAP object is created without error but seems to be incomplete.

sm = SAMAP(filenames, f_maps='maps/')

Processing data Bf from:
bf_processed-merged.fix.h5ad
RUNNING SAM
Iteration: 0, Convergence: 1.0
Iteration: 1, Convergence: 0.8185823941319791
Iteration: 2, Convergence: 0.03471146673392333
Computing the UMAP embedding...
Elapsed time: 440.5178737640381 seconds
Not updating the manifold...
Processing data Mm from:
mm_pijuan-sala.h5ad
RUNNING SAM
Iteration: 0, Convergence: 1.0
Iteration: 1, Convergence: 0.8812113103232017
Computing the UMAP embedding...
Elapsed time: 390.509724855423 seconds
Not updating the manifold...
17974 `Bf` gene symbols match between the datasets and the BLAST graph.
17757 `Mm` gene symbols match between the datasets and the BLAST graph.

I keep getting attribute errors while trying to run downstream analyses. For example, there is no attribute 'gnnm_refined':

sm.query_gene_pairs('Bf_bf-00014594')

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[14], line 2
      1 # Brachyury1
----> 2 sm.query_gene_pairs('bf-00014594')

File ~/mambaforge/envs/SAMap/lib/python3.9/site-packages/samap/mapping.py:518, in SAMAP.query_gene_pairs(self, gene)
    515     raise ValueError(f"Query gene {gene} not found in dataset.")
    517 a = self.gnnm[self.gns==qgene]
--> 518 b = self.gnnm_refined[self.gns==qgene]
    520 i1 = self.gns[a.nonzero()[1]]
    521 i2 = self.gns[b.nonzero()[1]]

AttributeError: 'SAMAP' object has no attribute 'gnnm_refined'

Upstream 'GNNMS_corr' also doesn't exist:

sm.GNNMS_corr

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[18], line 1
----> 1 sm.GNNMS_corr

AttributeError: 'SAMAP' object has no attribute 'GNNMS_corr'

Same with 'samap':

D,MappingTable = get_mapping_scores(sm,keys,n_top = 0)

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[16], line 2
      1 keys = {'Bf':'leiden_new', 'Mm':'celltype'}
----> 2 D,MappingTable = get_mapping_scores(sm,keys,n_top = 0)
      4 D.head()

File ~/mambaforge/envs/SAMap/lib/python3.9/site-packages/samap/analysis.py:1528, in get_mapping_scores(sm, keys, n_top)
   1526     samap = SAM(counts = sm.samap.adata[np.in1d(sm.samap.adata.obs['species'],list(keys.keys()))])
   1527 else:
-> 1528     samap=sm.samap
   1530 clusters = []
   1531 ix = np.unique(samap.adata.obs['species'],return_index=True)[1]

AttributeError: 'SAMAP' object has no attribute 'samap'

The SAMs (sm.sams do exist). Any idea what is going wrong here? Thanks.

[atarashansky]

Hi - you initialized the SAMAP object but didn't run anything. Check out the tutorial notebook for an example on how to run it!

[colinshew]

Sorry, easy fix. Thanks for your quick reply! Missed that line under the section for starting from SAMs.