Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

AttributeError: can't set attribute 'categories' #388

Open
BillyChen123 opened this issue Oct 29, 2023 · 0 comments
Open

AttributeError: can't set attribute 'categories' #388

BillyChen123 opened this issue Oct 29, 2023 · 0 comments

Comments

@BillyChen123
Copy link

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)...
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant