Add column in Obs. in anndata using scanpy
Entering edit mode
8 weeks ago
Nai ▴ 50

I separate the cells on the basis of a gene expression and now i would like to add column in obs where the genes are highly expressed then mention high and where it is low...then mentioned low. I am using anndata in scanpy

adata_H = adata_tumor[adata_tumor:, 'P53']. X > 0.5, :] adata_L = adata_tumor[adata_tumor:, 'P53']. X == 0, :] adata_tumor.obs["class"] = "high" adata_tumor.obs.loc[adata_L, "class"] = "low"

Then it shows

TypeError Traceback (most recent call last) /tmp/ipykernel_97150/ in <module> ----> 1 adata_TUMOR.obs.loc[low_1,'class'] = "low"

~/anaconda3/lib/python3.7/site-packages/pandas/core/ in __setitem__(self, key, value) 717 else: 718 key = com.apply_if_callable(key, self.obj) --> 719 indexer = self._get_setitem_indexer(key) 720 self._has_valid_setitem_indexer(key) 721

~/anaconda3/lib/python3.7/site-packages/pandas/core/ in _get_setitem_indexer(self, key) 658 if isinstance(key, tuple): 659 with suppress(IndexingError): --> 660 return self._convert_tuple(key, is_setter=True) 661 662 if isinstance(key, range):

~/anaconda3/lib/python3.7/site-packages/pandas/core/ in _convert_tuple(self, key, is_setter) 783 self._validate_key_length(key) 784 for i, k in enumerate(key): --> 785 idx = self._convert_to_indexer(k, axis=i, is_setter=is_setter) 786 keyidx.append(idx) 787

~/anaconda3/lib/python3.7/site-packages/pandas/core/ in _convert_to_indexer(self, key, axis, is_setter) 1258 else: 1259 try: -> 1260 return labels.get_loc(key) 1261 except LookupError: 1262 # allow a not found key only if we are a setter

~/anaconda3/lib/python3.7/site-packages/pandas/core/indexes/ in get_loc(self, key, method, tolerance) 3359 casted_key = self._maybe_cast_indexer(key) 3360 try: -> 3361 return self._engine.get_loc(casted_key) 3362 except KeyError as err: 3363 raise KeyError(key) from err

~/anaconda3/lib/python3.7/site-packages/pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

~/anaconda3/lib/python3.7/site-packages/pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

TypeError: 'View of AnnData object with n_obs × n_vars = 1679 × 33538 obs: 'age', 'barcode', 'batch', 'group', 'highest_GLEASON_score', 'mri_grading', 'name', 'patient', 'pool', 'psa', 'sample', 'scrublet_score', 'scrublet_cluster_score', 'bh_pval', 'is_doublet', 'n_genes', 'percent_mito', 'n_counts', 'S_score', 'G2M_score', 'phase', 'leiden', 'celltype', 'Biopsy Location DETAIL', 'Biopsy Location BRIEF', 'Biopsy Location Co-ordinate', 'PMHx', 'celltype-immune', 'class' var: 'gene_ids', 'feature_types' uns: 'celltype-immune_colors', 'celltype_colors', 'dendrogram_leiden', 'group_colors', 'leiden', 'neighbors', 'patient_colors', 'pca', 'phase_colors', 'rank_genes_groups', 'umap', 'leiden_colors' obsm: 'X_pca', 'X_umap' layers: 'cellranger_counts', 'soupx_counts'' is an invalid key

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