1877 del celldata.uns["spatial"] - error

[spatts14]

Hi,

I would really like to try to use this method on my Xenium spatial transcriptomics data that I've pre-processed with squidpy, however Im running into some issues.

Here is my Anndata object: _AnnData object with n_obs × n_vars = 53466 × 339 obs: 'cell_id', 'x_centroid', 'y_centroid', 'transcript_counts', 'control_probe_counts', 'control_codeword_counts', 'unassigned_codeword_counts', 'deprecated_codeword_counts', 'total_counts', 'cell_area', 'nucleus_area', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'log1p_total_counts', 'pct_counts_in_top_10_genes', 'pct_counts_in_top_20_genes', 'pct_counts_in_top_50_genes', 'n_counts', 'leiden_1.0', 'new_clusters', 'Cell_Type', 'Cluster', 'Condition', 'Sample_ID' var: 'gene_ids', 'feature_types', 'genome', 'n_cells_by_counts', 'mean_counts', 'log1p_mean_counts', 'pct_dropout_by_counts', 'total_counts', 'log1p_total_counts', 'n_cells' uns: 'dendrogram_leiden_1.0', 'leiden', 'leiden_1.0_colors', 'log1p', 'neighbors', 'new_clusters_colors', 'pca', 'rank_genes_groups', 'umap' obsm: 'X_pca', 'X_umap', 'spatial' varm: 'PCs' layers: 'rawcount' obsp: 'connectivities', 'distances'

This is the code I'm running

ncem.data = customLoader(
    adata=adata, cluster='new_cluster', patient='Sample_ID', library_id='None', radius=52
)
get_data_custom(interpreter=ncem)

Here is the error:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Cell In[7], [line 1](vscode-notebook-cell:?execution_count=7&line=1)
----> [1](vscode-notebook-cell:?execution_count=7&line=1) ncem.data = customLoader(
      [2](vscode-notebook-cell:?execution_count=7&line=2)     adata=adata, cluster='new_cluster', patient='Sample_ID', library_id='None', radius=52
      [3](vscode-notebook-cell:?execution_count=7&line=3) )
      [4](vscode-notebook-cell:?execution_count=7&line=4) get_data_custom(interpreter=ncem)

File [~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1852](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1852), in customLoader.__init__(self, adata, cluster, patient, library_id, radius, coord_type, n_rings, n_top_genes, label_selection)
   [1849](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1849) self.library_id = library_id
   [1851](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1851) print("Loading data from raw files")
-> [1852](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1852) self.register_celldata(n_top_genes=n_top_genes)
   [1853](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1853) self.register_img_celldata()
   [1854](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1854) self.register_graph_features(label_selection=label_selection)

File [~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1772](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1772), in DataLoader.register_celldata(self, n_top_genes)
   [1770](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1770) """Load AnnData object of complete dataset."""
   [1771](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1771) print("registering celldata")
-> [1772](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1772) self._register_celldata(n_top_genes=n_top_genes)
   [1773](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1773) assert self.celldata is not None, "celldata was not loaded"

File [~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1877](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1877), in customLoader._register_celldata(self, n_top_genes)
   [1875](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1875) celldata.X = celldata.X.toarray()
   [1876](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1876) celldata.uns["metadata"] = metadata
-> [1877](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1877) del celldata.uns["spatial"]
   [1879](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1879) # register node type names
   [1880](https://file+.vscode-resource.vscode-cdn.net/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/ST_Xenium_Asthma/scripts/~/opt/anaconda3/envs/ncem/lib/python3.8/site-packages/ncem/data.py:1880) node_type_names = list(np.unique(celldata.obs[self.cluster]))

KeyError: 'spatial'

Any suggestions on why Im getting this error?

System:

• OS: 14.2.1
• Language Version: Python 3.9
• Virtual environment: [e.g. Conda]