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.