Open Smilenone opened 5 months ago
I encountered an error when running sdm.extract_lr(adata, 'human', min_cell=3), following is the detailed issue:
sdm.weight_matrix(adata, l=1.2, cutoff=0.2, single_cell=False) # weight_matrix by rbf kernel ----> 3 sdm.extract_lr(adata, 'human', min_cell=3) # find overlapping LRs from CellChatDB 5 sdm.spatialdm_global(adata, 1000, specified_ind=None, method='both', nproc=1) # global Moran selection 6 sdm.sig_pairs(adata, method='permutation', fdr=True, threshold=0.1) # select significant pairs File ~\AppData\Roaming\Python\Python39\site-packages\spatialdm\main.py:149, in extract_lr(adata, species, mean, min_cell, datahost) 147 meanR = gmean(adata[:, receptor[i]].X, axis=1) 148 else: --> 149 meanL = adata[:, ligand[i]].X.mean(axis=1) 150 meanR = adata[:, receptor[i]].X.mean(axis=1) 151 if (sum(meanL > 0) >= min_cell) * \ 152 (sum(meanR > 0) >= min_cell): File ~\AppData\Roaming\Python\Python39\site-packages\anndata\_core\anndata.py:1108, in AnnData.__getitem__(self, index) 1106 def __getitem__(self, index: Index) -> "AnnData": 1107 """Returns a sliced view of the object.""" -> 1108 oidx, vidx = self._normalize_indices(index) 1109 return AnnData(self, oidx=oidx, vidx=vidx, asview=True) File ~\AppData\Roaming\Python\Python39\site-packages\anndata\_core\anndata.py:1089, in AnnData._normalize_indices(self, index) 1088 def _normalize_indices(self, index: Optional[Index]) -> Tuple[slice, slice]: -> 1089 return _normalize_indices(index, self.obs_names, self.var_names) File ~\AppData\Roaming\Python\Python39\site-packages\anndata\_core\index.py:33, in _normalize_indices(index, names0, names1) 31 ax0, ax1 = unpack_index(index) 32 ax0 = _normalize_index(ax0, names0) ---> 33 ax1 = _normalize_index(ax1, names1) 34 return ax0, ax1 File ~\AppData\Roaming\Python\Python39\site-packages\anndata\_core\index.py:95, in _normalize_index(indexer, index) 93 return positions # np.ndarray[int] 94 else: # indexer should be string array ---> 95 positions = index.get_indexer(indexer) 96 if np.any(positions < 0): 97 not_found = indexer[positions < 0] File ~\AppData\Roaming\Python\Python39\site-packages\pandas\core\indexes\base.py:3904, in Index.get_indexer(self, target, method, limit, tolerance) 3901 self._check_indexing_method(method, limit, tolerance) 3903 if not self._index_as_unique: -> 3904 raise InvalidIndexError(self._requires_unique_msg) 3906 if len(target) == 0: 3907 return np.array([], dtype=np.intp) InvalidIndexError: Reindexing only valid with uniquely valued Index objects
Can you help?
It seems like you should check your adata object. Can you run the tutorial successfully?
I think you can check whether there are duplicate gene names in your 'adata.var'.
I encountered an error when running sdm.extract_lr(adata, 'human', min_cell=3), following is the detailed issue:
Can you help?