sc.pl.heatmap var_names function KeyError #3363
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@josenimo Judging by our tests, the and @flying-sheep thoughts? |
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Ah I think I understand better. |
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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
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