unexpected keyword argument 'validated_adjacency_key'

[ChloeHJ]

Hi,

Thanks for an amazing package. I was trying to run tutorial on pancreatic_islets_scrnaseq_example and I was getting errors:
fs.tl.apply_biological_flow(adata,
flowsig_network_key = 'flowsig_network',
adjacency_key = 'adjacency',
validated_adjacency_key = 'adjacency_validated'
)
TypeError: apply_biological_flow() got an unexpected keyword argument 'validated_adjacency_key'

I've tried changing the argument based on the latest code, but still giving me error
fs.tl.apply_biological_flow(adata,
flowsig_network_key = 'flowsig_network',
adjacency_key = 'adjacency',
validated_key = 'validated'
)

          163 # Get the adjacency
      --> 164 adjacency = adata.uns[flowsig_network_key]['network'][adjacency_key]
          165 flow_vars = adata.uns[flowsig_network_key]['flow_var_info'].index.tolist()
          166 flow_var_info = adata.uns[flowsig_network_key]['flow_var_info']
      
      KeyError: 'network'

Similarly, the code below as throwing out error as well:
edge_threshold = 0.7
fs.tl.filter_low_confidence_edges(adata,
edge_threshold = edge_threshold,
flowsig_network_key = 'flowsig_network',
adjacency_key = 'adjacency',
filtered_adjacency_key = 'adjacency_filtered')
TypeError: filter_low_confidence_edges() got an unexpected keyword argument 'filtered_adjacency_key'

Are these still under development? I would love to give it a try but wasn't sure if they are not yet ready for use

Thanks and best wishes
Chloe

[axelalmet]

Hi Chloe,

Thanks for the question and I'm very sorry for taking so long to respond!

I reran the pancreatic islets example and didn't get this error. The only reason I can think of why you have this issue is that, for some reason, the output of fs.tl.learn_intercellular_flows hasn't been saved correctly. Would you mind rerunning learn_intercellular_flows and then trying to run fs.tl.apply_biological_flow and fs.tl.filter_low_confidence_edges?

You have however pointed out correctly that the tutorial is out of date regarding the command arguments to specify for fs.tl.apply_biological_flow and fs.tl.filter_low_confidence_edges. I've updated the tutorial in flowsig repository to reflect those changes. Thanks for catching that!

Best wishes,
Axel.

[BlanQwall]

Hi Axel, I just got the same issue. I check the function's arguments. It seems that there's no validated_adjacency_key but validated_key for apply_biological_flow, and no filtered_adjacency_key but filtered_key for filter_low_confidence_edges. Maybe that's the reason?

[axelalmet]

Hi ChloeHJ and BlanQwall,

Very sorry for my extremely late reply. You're completely right! The README.md has the correct commands but the tutorials were wrong. I have updated the tutorial notebooks/scripts so that they have the right arguments specified.

Best wishes,
Axel.