You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I have checked that this issue has not already been reported.
I have confirmed this bug exists on the latest version of scanpy.
(optional) I have confirmed this bug exists on the main branch of scanpy.
What happened?
I pass a adata.var column header with my gene name that I want displayed, sc.pl.heatmap runs into a key error where my index values are being searched in the genename column
Please make sure these conditions are met
What happened?
I pass a adata.var column header with my gene name that I want displayed, sc.pl.heatmap runs into a key error where my index values are being searched in the genename column
Minimal code sample
Error output
--------------------------------------------------------------------------- KeyError Traceback (most recent call last) Cell In[86], line 1 ----> 1 sc.pl.heatmap( 2 adata=adata, 3 var_names=top_25, 4 gene_symbols=adata.var.columns.tolist()[2], 5 groupby='slide_number', 6 swap_axes=True, 7 standard_scale='var', 8 ) File /opt/homebrew/Caskroom/mambaforge/base/envs/proteomics/lib/python3.12/site-packages/legacy_api_wrap/__init__.py:80, in legacy_api.<locals>.wrapper.<locals>.fn_compatible(*args_all, **kw) 77 @wraps(fn) 78 def fn_compatible(*args_all: P.args, **kw: P.kwargs) -> R: 79 if len(args_all) <= n_positional: ---> 80 return fn(*args_all, **kw) 82 args_pos: P.args 83 args_pos, args_rest = args_all[:n_positional], args_all[n_positional:] File /opt/homebrew/Caskroom/mambaforge/base/envs/proteomics/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:1120, in heatmap(adata, var_names, groupby, use_raw, log, num_categories, dendrogram, gene_symbols, var_group_positions, var_group_labels, var_group_rotation, layer, standard_scale, swap_axes, show_gene_labels, show, save, figsize, vmin, vmax, vcenter, norm, **kwds) 1070 """\ 1071 Heatmap of the expression values of genes. 1072 (...) 1114 tl.rank_genes_groups 1115 """ 1116 var_names, var_group_labels, var_group_positions = _check_var_names_type( 1117 var_names, var_group_labels, var_group_positions 1118 ) -> 1120 categories, obs_tidy = _prepare_dataframe( 1121 adata, 1122 var_names, 1123 groupby, 1124 use_raw=use_raw, 1125 log=log, 1126 num_categories=num_categories, 1127 gene_symbols=gene_symbols, 1128 layer=layer, 1129 ) 1131 # check if var_group_labels are a subset of categories: 1132 if var_group_labels is not None: File /opt/homebrew/Caskroom/mambaforge/base/envs/proteomics/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:2057, in _prepare_dataframe(adata, var_names, groupby, use_raw, log, num_categories, layer, gene_symbols) 2055 groupby.remove(groupby_index) 2056 keys = list(groupby) + list(np.unique(var_names)) -> 2057 obs_tidy = get.obs_df( 2058 adata, keys=keys, layer=layer, use_raw=use_raw, gene_symbols=gene_symbols 2059 ) 2060 assert np.all(np.array(keys) == np.array(obs_tidy.columns)) 2062 if groupby_index is not None: 2063 # reset index to treat all columns the same way. File /opt/homebrew/Caskroom/mambaforge/base/envs/proteomics/lib/python3.12/site-packages/scanpy/get/get.py:296, in obs_df(adata, keys, obsm_keys, layer, gene_symbols, use_raw) 293 else: 294 alias_index = None --> 296 obs_cols, var_idx_keys, var_symbols = _check_indices( 297 adata.obs, 298 var.index, 299 dim="obs", 300 keys=keys, 301 alias_index=alias_index, 302 use_raw=use_raw, 303 ) 305 # Make df 306 df = pd.DataFrame(index=adata.obs_names) File /opt/homebrew/Caskroom/mambaforge/base/envs/proteomics/lib/python3.12/site-packages/scanpy/get/get.py:186, in _check_indices(dim_df, alt_index, dim, keys, alias_index, use_raw) 184 not_found.append(key) 185 if len(not_found) > 0: --> 186 raise KeyError( 187 f"Could not find keys '{not_found}' in columns of `adata.{dim}` or in" 188 f" {alt_repr}.{alt_search_repr}." 189 ) 191 return col_keys, index_keys, index_aliases KeyError: "Could not find keys '[np.str_('O00154'), np.str_('O00515'), np.str_('O94886'), np.str_('P09493'), np.str_('P20338'), np.str_('P23141'), np.str_('P49419'), np.str_('P55268'), np.str_('P98095'), np.str_('P98160'), np.str_('Q01995'), np.str_('Q05682'), np.str_('Q09666'), np.str_('Q13751'), np.str_('Q14195'), np.str_('Q16795'), np.str_('Q8IUX7'), np.str_('Q8WX93'), np.str_('Q96AC1'), np.str_('Q96FZ7'), np.str_('Q96G03'), np.str_('Q9NSE4'), np.str_('Q9NZM1'), np.str_('Q9UN36'), np.str_('Q9Y4K1')]' in columns of `adata.obs` or in adata.var['Genes']."Versions
The text was updated successfully, but these errors were encountered: