Met problems when using tc.tl.annotate()

When I use tc.tl.annotate(), where the ref and space data was read by scanpy. I met the following error:

InvalidIndexError Traceback (most recent call last) Input In [7], in <cell line: 1>() ----> 1 tc.tl.annotate(adata_spatial, reference,'celltype1',result_key='celltype1',)

File D:\Basic Tools\Anaconda\lib\site-packages\tacco\tools_annotate.py:734, in annotate(adata, reference, annotation_key, result_key, counts_location, method, bisections, bisection_divisor, platform_iterations, normalize_to, annotation_prior, multi_center, multi_center_amplitudes, reconstruction_key, max_annotation, min_counts_per_gene, min_counts_per_cell, min_cells_per_gene, min_genes_per_cell, remove_constant_genes, remove_zero_cells, min_log2foldchange, min_expression, remove_mito, n_hvg, skip_checks, assume_valid_counts, return_reference, gene_keys, verbose, **kw_args) 732 except ValueError as e: # as e syntax added in ~python2.5 733 raise ValueError(f'{str(e)}\nYou can deactivate checking for invalid counts by specifying assume_valid_counts=True.') --> 734 tdata,reference = preprocessing.filter(adata=(tdata,reference), min_counts_per_cell=min_counts_per_cell, min_counts_per_gene=min_counts_per_gene, min_cells_per_gene=min_cells_per_gene, min_genes_per_cell=min_genes_per_cell, remove_constant_genes=remove_constant_genes, remove_zero_cells=remove_zero_cells, assume_valid_counts=True) # ensure consistent gene selection 735 if verbose > 0: 736 print(f'Finished preprocessing in {np.round(time.time() - start, 2)} seconds.')

File D:\Basic Tools\Anaconda\lib\site-packages\tacco\preprocessing_qc.py:163, in filter(adata, min_counts_per_gene, min_counts_per_cell, min_cells_per_gene, min_genes_per_cell, remove_constant_genes, remove_zero_cells, assume_valid_counts, return_view) 161 for i in range(len(adatas)): 162 if len(adatas[i].var.index) != len(good_genes): # filter happened --> 163 adatas[i] = adatas[i][:,good_genes] 164 changed = True 165 elif (adatas[i].var.index != good_genes).any(): # reordering happened: no side effects on cell filtering

File D:\Basic Tools\Anaconda\lib\site-packages\anndata_core\anndata.py:1113, in AnnData.getitem(self, index) 1111 def getitem(self, index: Index) -> "AnnData": 1112 """Returns a sliced view of the object.""" -> 1113 oidx, vidx = self._normalize_indices(index) 1114 return AnnData(self, oidx=oidx, vidx=vidx, asview=True)

File D:\Basic Tools\Anaconda\lib\site-packages\anndata_core\anndata.py:1094, in AnnData._normalize_indices(self, index) 1093 def _normalize_indices(self, index: Optional[Index]) -> Tuple[slice, slice]: -> 1094 return _normalize_indices(index, self.obs_names, self.var_names)

File D:\Basic Tools\Anaconda\lib\site-packages\anndata_core\index.py:36, in _normalize_indices(index, names0, names1) 34 ax0, ax1 = unpack_index(index) 35 ax0 = _normalize_index(ax0, names0) ---> 36 ax1 = _normalize_index(ax1, names1) 37 return ax0, ax1

File D:\Basic Tools\Anaconda\lib\site-packages\anndata_core\index.py:98, in _normalize_index(indexer, index) 96 return positions # np.ndarray[int] 97 else: # indexer should be string array ---> 98 positions = index.get_indexer(indexer) 99 if np.any(positions < 0): 100 not_found = indexer[positions < 0]

File D:\Basic Tools\Anaconda\lib\site-packages\pandas\core\indexes\base.py:3905, in Index.get_indexer(self, target, method, limit, tolerance) 3902 self._check_indexing_method(method, limit, tolerance) 3904 if not self._index_as_unique: -> 3905 raise InvalidIndexError(self._requires_unique_msg) 3907 if len(target) == 0: 3908 return np.array([], dtype=np.intp)

InvalidIndexError: Reindexing only valid with uniquely valued Index objects

Can you help?

simonwm / tacco

Met problems when using tc.tl.annotate() #3