Open BillyChen123 opened 9 months ago
Why did I run desc method has a attribute issue? I have never met it before.
datasets = sc.read_h5ad(filepath) datasets.obs['Batch'] = pd.CategoricalIndex(datasets.obs['Batch']) datasets.obs['Batch2'] = pd.CategoricalIndex(datasets.obs['Batch2']) datasets.obs['Group'] = pd.CategoricalIndex(datasets.obs['Group']) sc.pp.normalize_total(datasets,target_sum= 1e4) sc.pp.log1p(datasets) sc.pp.highly_variable_genes(datasets) #sc.pl.highly_variable_genes(datasets) adata = scib.integration.desc(datasets,'Batch2',res = 0.8)``` AttributeError Traceback (most recent call last) /home/chenyz/Matrix_Factorization/rank/Untitled-1.ipynb 单元格 2 line 1 [8](vscode-notebook-cell://ssh-remote%2B10.181.6.84/home/chenyz/Matrix_Factorization/rank/Untitled-1.ipynb#W5sdnNjb2RlLXJlbW90ZQ%3D%3D?line=7) sc.pp.highly_variable_genes(datasets) [9](vscode-notebook-cell://ssh-remote%2B10.181.6.84/home/chenyz/Matrix_Factorization/rank/Untitled-1.ipynb#W5sdnNjb2RlLXJlbW90ZQ%3D%3D?line=8) #sc.pl.highly_variable_genes(datasets) ---> [10](vscode-notebook-cell://ssh-remote%2B10.181.6.84/home/chenyz/Matrix_Factorization/rank/Untitled-1.ipynb#W5sdnNjb2RlLXJlbW90ZQ%3D%3D?line=9) adata = scib.integration.desc(datasets,'Batch2',res = 0.8) File [~/anaconda3/envs/MOBA_Billy/lib/python3.10/site-packages/scib/integration.py:449](https://vscode-remote+ssh-002dremote-002b10-002e181-002e6-002e84.vscode-resource.vscode-cdn.net/home/chenyz/Matrix_Factorization/rank/~/anaconda3/envs/MOBA_Billy/lib/python3.10/site-packages/scib/integration.py:449), in desc(adata, batch, res, ncores, tmp_dir, use_gpu) 445 adata_out = adata.copy() 447 adata_out = desc.scale_bygroup(adata_out, groupby=batch, max_value=6) --> 449 adata_out = desc.train( 450 adata_out, 451 dims=[adata.shape[1], 128, 32], 452 tol=0.001, 453 n_neighbors=10, 454 batch_size=256, 455 louvain_resolution=res, 456 save_encoder_weights=False, 457 save_dir=tmp_dir, 458 do_tsne=False, 459 use_GPU=use_gpu, 460 num_Cores=ncores, 461 use_ae_weights=False, 462 do_umap=False, 463 ) ... File [~/anaconda3/envs/MOBA_Billy/lib/python3.10/site-packages/pandas/core/arrays/categorical.py:2867](https://vscode-remote+ssh-002dremote-002b10-002e181-002e6-002e84.vscode-resource.vscode-cdn.net/home/chenyz/Matrix_Factorization/rank/~/anaconda3/envs/MOBA_Billy/lib/python3.10/site-packages/pandas/core/arrays/categorical.py:2867), in CategoricalAccessor._delegate_property_set(self, name, new_values) 2866 def _delegate_property_set(self, name: str, new_values): # type: ignore[override] -> 2867 return setattr(self._parent, name, new_values) AttributeError: can't set attribute 'categories' Output is truncated. View as a [scrollable element](command:cellOutput.enableScrolling?1599f676-8fcd-4683-a362-9a7106fbf73d) or open in a [text editor](command:workbench.action.openLargeOutput?1599f676-8fcd-4683-a362-9a7106fbf73d). Adjust cell output [settings](command:workbench.action.openSettings?%5B%22%40tag%3AnotebookOutputLayout%22%5D)...
Why did I run desc method has a attribute issue? I have never met it before.