fs.pp.construct_flows_from_cellchat error

[xy441]

Hello, I referred to your method and ran a similar program, but it reported an error and could not be solved. I reused 1 10,000 cells with no errors. The error data was about 200,000 cells. How should I deal with it?

fs.pp.construct_flows_from_cellchat(adata,cellchat_output_key,gem_expr_key = 'X_gem',scale_gem_expr=True,model_organism='human',flowsig_network_key='flowsig_network',flowsig_expr_key='X_flow')

error:
IndexError Traceback (most recent call last)
Cell In[35], line 1
----> 1 fs.pp.construct_flows_from_cellchat(adata,cellchat_output_key,gem_expr_key = 'X_gem',scale_gem_expr=True,model_organism='human',flowsig_network_key='flowsig_network',flowsig_expr_key='X_flow')

File ~/miniconda3/envs/FlowSig/lib/python3.11/site-packages/flowsig/preprocessing/_flow_expressions.py:243, in construct_flows_from_cellchat(adata, cellchat_output_key, gem_expr_key, scale_gem_expr, model_organism, flowsig_network_key, flowsig_expr_key)
231 def construct_flows_from_cellchat(adata: sc.AnnData,
232 cellchat_output_key: str,
233 gem_expr_key: str = 'X_gem',
(...)
239
240 # Define the expression
241 adata_outflow, outflow_vars = construct_outflow_signals_cellchat(adata, cellchat_output_key)
--> 243 adata_inflow, inflow_vars = construct_inflow_signals_cellchat(adata, cellchat_output_key, model_organism)
245 adata_gem, flow_gem_vars = construct_gem_expressions(adata, gem_expr_key, scale_gem_expr)
247 # Determine the flow_variables

File ~/miniconda3/envs/FlowSig/lib/python3.11/site-packages/flowsig/preprocessing/flow_expressions.py:73, in construct_inflow_signals_cellchat(adata, cellchat_output_key, model_organism)
70 if rec not in adata.var_names:
71 receptor_v2_split = ccc_output_merged[ccc_output_merged['interaction_name_2'] == interaction]['receptor'].unique()[0].split('')
---> 73 receptors.append(receptor_v2_split[i])
74 else:
75 receptors.append(rec)

IndexError: list index out of range

[hajihajilala]

Hi xy441,
I have encountered this question. I check CellChat output dataframe and find "CD8 receptor" in the column "receptor", it's the reason error happened. I try to change "CD8 receptor" into "CD8A_CD8B1" in column "receptor" in the CellChat output. And then it's run complete.