AttributeError: 'AnnData' object has no attribute 'flatten'

[WangShuai-3]

Hello, I encountered an error while running the following code:

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

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In [16], line 1
----> 1 fs.pp.construct_flows_from_cellchat(data,
      2                                 cellchat_output_key,
      3                                 gem_expr_key = 'X_gem',
      4                                 scale_gem_expr = False,
      5                                 model_organism = 'human',
      6                                 flowsig_network_key = 'flowsig_network',
      7                                 flowsig_expr_key = 'X_flow')

File /opt/conda/lib/python3.8/site-packages/flowsig/preprocessing/_flow_expressions.py:263, in construct_flows_from_cellchat(adata, cellchat_output_key, gem_expr_key, scale_gem_expr, model_organism, flowsig_network_key, flowsig_expr_key)
    260     flow_downstream_tfs[outflow_var] = adata_gem.var['downstream_tfs'].loc[gem]
    261     flow_interactions[outflow_var] = adata_gem.var['interactions'].loc[gem]
--> 263     flow_expressions[:, len(outflow_vars) + len(inflow_vars) + i] = adata_gem[:, gem].flatten()
    265 # Store the type, relevant downstream_TF, and received interactions for each variable
    266 # Store all the information on the flow variables
    267 adata.uns[flowsig_network_key] = {'flow_vars': flow_variables,
    268                                   'flow_var_types': flow_variable_types,
    269                                   'downstream_tfs': flow_downstream_tfs,
    270                                   'interactions': flow_interactions
    271                                   }

AttributeError: 'AnnData' object has no attribute 'flatten'

The issue seems to be at line 263 in _flow_expressions.py. The expression adata_gem[:, gem].flatten() should be modified to adata_gem[:, gem].X.flatten() because adata_gem is an AnnData object. Is that correct?

[axelalmet]

Hello,

This error seems to be from an older version of FlowSig, as you can see that, as you correctly pointed out, it is indeed adam_gem[:, gem].X.flatten() here.

[WangShuai-3]

I reinstalled flowsig and it works now. thanks!

[LJZYaaa]

HI, I just face the same problem as yours. And the flowsig i install just as the tutorial use the setup.py. Could you ples tell me how to update it? Any advice will be appreciated :) @WangShuai-3 @axelalmet

[WangShuai-3]

I used mirror.ghproxy.com to clone this repository before, but when I cloned it again without the mirror, the issue didn’t come up. I’m not sure if the problem is with mirror.ghproxy.com, but re-cloning the repository might fix it. @LJZYaaa