TypeError: Passing a set as an indexer is not supported. Use a list instead.

[Fanyu000]

Hello, I encoutered a warning today with this code interactions = c2c.analysis.SingleCellInteractions(rnaseq_data=rnaseq.to_df().T, ppi_data=lr_pairs, metadata=meta, interaction_columns=('ligand_symbol', 'receptor_symbol'), communication_score='expression_thresholding', expression_threshold=0.1, # values after aggregation cci_score='bray_curtis', cci_type='undirected', aggregation_method='nn_cell_fraction', barcode_col='index', celltype_col='celltype', complex_sep='&', verbose=False)

And it warns me like that

TypeError Traceback (most recent call last) Cell In[12], line 1 ----> 1 interactions = c2c.analysis.SingleCellInteractions(rnaseq_data=rnaseq.to_df().T, 2 ppi_data=lr_pairs, 3 metadata=meta, 4 interaction_columns=('ligand2', 'receptor2'), 5 communication_score='expression_thresholding', 6 expression_threshold=0.1, # values after aggregation 7 cci_score='bray_curtis', 8 cci_type='undirected', 9 aggregation_method='nn_cell_fraction', 10 barcode_col='index', 11 celltype_col='cell_type', 12 complex_sep='&', 13 verbose=False)

File D:\anaconda\Lib\site-packages\cell2cell\analysis\cell2cell_pipelines.py:693, in SingleCellInteractions.init(self, rnaseq_data, ppi_data, metadata, interaction_columns, communication_score, cci_score, cci_type, expression_threshold, aggregation_method, barcode_col, celltype_col, complex_sep, complex_agg_method, verbose) 685 self.aggregated_expression = rnaseq.aggregate_single_cells(rnaseq_data=self.rnaseq_data, 686 metadata=self.metadata, 687 barcode_col=self.index_col, 688 celltype_col=self.group_col, 689 method=self.aggregation_method, 690 transposed=self.__adata) 692 # Interaction Space --> 693 self.interaction_space = initialize_interaction_space(rnaseq_data=self.aggregated_expression, 694 ppi_data=self.ppi_data, 695 cutoff_setup=self.cutoff_setup, 696 analysis_setup=self.analysis_setup, 697 complex_sep=self.complex_sep, 698 complex_agg_method=self.complex_agg_method, 699 interaction_columns=self.interaction_columns, 700 verbose=verbose)

File D:\anaconda\Lib\site-packages\cell2cell\analysis\cell2cell_pipelines.py:940, in initialize_interaction_space(rnaseq_data, ppi_data, cutoff_setup, analysis_setup, excluded_cells, complex_sep, complex_agg_method, interaction_columns, verbose) 936 excluded_cells = [] 938 included_cells = sorted(list((set(rnaseq_data.columns) - set(excluded_cells)))) --> 940 interaction_space = ispace.InteractionSpace(rnaseq_data=rnaseq_data[included_cells], 941 ppi_data=ppi_data, 942 gene_cutoffs=cutoff_setup, 943 communication_score=analysis_setup['communication_score'], 944 cci_score=analysis_setup['cci_score'], 945 cci_type=analysis_setup['cci_type'], 946 complex_sep=complex_sep, 947 complex_agg_method=complex_agg_method, 948 interaction_columns=interaction_columns, 949 verbose=verbose) 950 return interaction_space

File D:\anaconda\Lib\site-packages\cell2cell\core\interaction_space.py:381, in InteractionSpace.init(self, rnaseq_data, ppi_data, gene_cutoffs, communication_score, cci_score, cci_type, cci_matrix_template, complex_sep, complex_agg_method, interaction_columns, verbose) 374 self.ppi_data = self.ppi_data.assign(score=1.0) 376 self.modified_rnaseq = integrate_data.get_modified_rnaseq(rnaseq_data=rnaseq_data, 377 cutoffs=cutoff_values, 378 communication_score=self.communication_score, 379 ) --> 381 self.interaction_elements = generate_interaction_elements(modified_rnaseq=self.modified_rnaseq, 382 ppi_data=self.ppi_data, 383 cci_matrix_template=cci_matrix_template, 384 cci_type=self.cci_type, 385 complex_sep=complex_sep, 386 complex_agg_method=complex_agg_method, 387 verbose=verbose) 389 self.interaction_elements['ppi_score'] = self.ppi_data['score'].values

File D:\anaconda\Lib\site-packages\cell2cell\core\interaction_space.py:146, in generate_interaction_elements(modified_rnaseq, ppi_data, cci_type, cci_matrix_template, complex_sep, complex_agg_method, interaction_columns, verbose) 141 if complex_sep is not None: 142 col_a_genes, complex_a, col_b_genes, complex_b, complexes = get_genes_from_complexes(ppi_data=ppi_data, 143 complex_sep=complex_sep, 144 interaction_columns=interaction_columns 145 ) --> 146 modified_rnaseq = add_complexes_to_expression(rnaseq_data=modified_rnaseq, 147 complexes=complexes, 148 agg_method=complex_agg_method 149 ) 151 # Cells 152 cell_instances = list(modified_rnaseq.columns) # @Erick, check if position 0 of columns contain index header.

File D:\anaconda\Lib\site-packages\cell2cell\preprocessing\rnaseq.py:179, in add_complexes_to_expression(rnaseq_data, complexes, agg_method) 177 for k, v in complexes.items(): 178 if all(g in tmp_rna.index for g in v): --> 179 df = tmp_rna.loc[v, :] 180 if agg_method == 'min': 181 tmp_rna.loc[k] = df.min().values.tolist()

File D:\anaconda\Lib\site-packages\pandas\core\indexing.py:1091, in _LocationIndexer.getitem(self, key) 1089 @final 1090 def getitem(self, key): -> 1091 check_dict_or_set_indexers(key) 1092 if type(key) is tuple: 1093 key = tuple(list(x) if is_iterator(x) else x for x in key)

File D:\anaconda\Lib\site-packages\pandas\core\indexing.py:2618, in check_dict_or_set_indexers(key) 2610 """ 2611 Check if the indexer is or contains a dict or set, which is no longer allowed. 2612 """ 2613 if ( 2614 isinstance(key, set) 2615 or isinstance(key, tuple) 2616 and any(isinstance(x, set) for x in key) 2617 ): -> 2618 raise TypeError( 2619 "Passing a set as an indexer is not supported. Use a list instead." 2620 ) 2622 if ( 2623 isinstance(key, dict) 2624 or isinstance(key, tuple) 2625 and any(isinstance(x, dict) for x in key) 2626 ): 2627 raise TypeError( 2628 "Passing a dict as an indexer is not supported. Use a list instead." 2629 )

TypeError: Passing a set as an indexer is not supported. Use a list instead.

how can I deal with it. my RANseq datafrme is like the screenshots show

Thanks

[earmingol]

I suggest doing this before calling cell2cell meta.index.name = 'barcodes'

Then replace this barcode_col='index' by barcode_col='barcodes' when calling c2c.analysis.SingleCellInteractions()

In case this does not work, do you have a screenshot of the dataframe for the ligand-receptor pairs? Also it would be useful if you check if you have repeated gene names in your data, for that use this:

rnaseq_df = rnaseq.to_df().T
rnaseq_df[~rnaseq_df.index.duplicated()]

Then pass rnaseq_df into

interactions = c2c.analysis.SingleCellInteractions(rnaseq_data=rnaseq_df,
ppi_data=lr_pairs,
metadata=meta,
interaction_columns=('ligand_symbol', 'receptor_symbol'),
communication_score='expression_thresholding',
expression_threshold=0.1, # values after aggregation
cci_score='bray_curtis',
cci_type='undirected',
aggregation_method='nn_cell_fraction',
barcode_col='barcodes',
celltype_col='celltype',
complex_sep='&',
verbose=False)

Also what version of pandas are you using? I think that could be also a reason for this error.

If this does not work, send me an email to erickarmingol [AT] gmail.com, and I would be happy to help.

[Fanyu000]

@earmingol I have sent you the email with your needed information. It still can't work.

[earmingol]

I haven't got your email, but I think the error could be due to the version of pandas. From version 1.5 is not supporting sets to call indexes anymore. I need to push an update for fixing this. In the meantime, if your pandas version is 1.5 or higher, try installing an older version with pip install -U pandas<1.5

[Pangjing-Wu]

In another issue I found a way that may help you solve this error. Maybe you can try it.

[earmingol]

As @Pangjing-Wu pointed out, the issue was due to the lost of support for using sets for indexing in pandas. I just implemented a fix for this. Please update to v0.7.4 with pip install -U cell2cell.