KeyError: (19, 11)" AND AttributeError: module 'flowsig.plotting' has no attribute 'plot_differentially_flowing_signals'"

[YuNong-Qiu]

Dear Author,
I encountered some issues while executing the code.

When I used the function 'fs.tl.construct_intercellular_flow_network(adata_dis, flowsig_network_key='flowsig_network', adjacency_key='adjacency_validated_filtered')', I encountered a KeyError. And I have checked the data 'adata_dis.uns['flowsig_network']['network']['adjacency_validated_filtered']', but it seemed no problem.

And I am unable to generate the plot using 'fs.pl.plot_differentially_flowing_signals'. The code and the error message are below.

I am eagerly awaiting your guidance on this matter. Thank you in advance for your assistance!

--1--
CODE:
flow_network = fs.tl.construct_intercellular_flow_network(adata_dis,
flowsig_network_key = 'flowsig_network',
adjacency_key = 'adjacency_validated_filtered')

{
"name": "KeyError",
"message": "(19, 11)",
"stack": "---------------------------------------------------------------------------

OUTPUT:
KeyError Traceback (most recent call last)
Cell In[51], line 1
----> 1 flow_network = fs.tl.construct_intercellular_flow_network(adata_dis,
2 flowsig_network_key = 'flowsig_network',
3 adjacency_key = 'adjacency_validated_filtered')

File c:\Users\Q\.conda\envs\COMMOT\Lib\site-packages\flowsig\tools\_validate_network.py:380, in construct_intercellular_flow_network(adata, flowsig_network_key, adjacency_key)
376 total_edge_weight = total_edge_weights[undirected_edge]
378 else:
--> 380 total_edge_weight = total_edge_weights[(undirected_edge[1], undirected_edge[0])]
382 flow_network.add_edge(*undirected_edge)
383 flow_network.edges[undirected_edge[0], undirected_edge[1]]['weight'] = min(total_edge_weight, 1.0)

KeyError: (19, 11)"
}

--2--
CODE:
fs.pl.plot_differentially_flowing_signals(
adata = adata_dis,
condition_key = 'Condition',
pert_key = 'GAS6',
var_type = 'inflow',
flowsig_expr_key = 'X_flow',
flowsig_network_key = 'flowsig_network_orig',
qval_threshold = 0.05,
logfc_threshold = 0.5,
label_lowqval = True
)

OUTPUT:
{
"name": "AttributeError",
"message": "module 'flowsig.plotting' has no attribute 'plot_differentially_flowing_signals'",
"stack": "---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[80], line 1
----> 1 fs.pl.plot_differentially_flowing_signals(
2 adata = adata_dis,
3 condition_key = 'Condition',
4 pert_key = 'GAS6',
5 var_type = 'inflow',
6 flowsig_expr_key = 'X_flow',
7 flowsig_network_key = 'flowsig_network_orig',
8 qval_threshold = 0.05,
9 logfc_threshold = 0.5,
10 label_lowqval = True
11 )

AttributeError: module 'flowsig.plotting' has no attribute 'plot_differentially_flowing_signals'"
}

[yang-lin-pp]

Hello! Have you solved it? I also got this when flowsig running. Can I ask for the solution?

[YuNong-Qiu]

@yang-lin-pp
For the first question about a "keyError" , I tried to add a new conditional check so that if it's not in the key, it can be set to a default value in the 'construct_intercellular_flow_network' function.
For more details, you can refer to the function in flowsig/tools/_validate_network.py. On line 373, I have added a 'else' like：

if add_edge:
# Get the total edge weight
total_edge_weight = 0.0
edge_key = undirected_edge
reversed_edge_key = (undirected_edge[1], undirected_edge[0])

    if edge_key in total_edge_weights:
        total_edge_weight = total_edge_weights[edge_key]
    elif reversed_edge_key in total_edge_weights:
        total_edge_weight = total_edge_weights[reversed_edge_key]
    else:
        # Handle the case where the edge is not found in total_edge_weights
        # You can set a default value or handle the error as needed
        total_edge_weight = 1.0  # Example default value

However, I am uncertain whether this approach is reasonable. This may potentially affect some outcomes。

For the second question，I haven't figured out it yet.

[axelalmet]

Hi @YuNong-Qiu,

First up, sorry about the late response! You did nothing wrong, but I hadn't fully implemented pl.plot_differentially_flowing_signals yet. But with the latest version (0.1.2,), I finally added the plotting functions.

So now, if you want to plot the differentially inflowing variables, try calling something like:

fig, ax = plt.subplots(figsize=(6, 4))
fs.pl.plot_differentially_flowing_signals(adata = adata_dis,
                                                                condition_key = 'Condition',
                                                                pert_key = 'GAS6',
                                                                var_type = 'inflow',
                                                                flowsig_expr_key = 'X_flow_orig',
                                                                flowsig_network_key = 'flowsig_network_orig',
                                                                qval_threshold = 0.05,
                                                                logfc_threshold = 0.5,
                                                                label_lowqval = True,
                                                                ax=ax
                                                                )
plt.show()

Note that you have to set flowsig_expr_key = X_flow_orig to show the non-significantly flowing variable.s

I'll update the README.md to include an example and add a notebook example to show how you can use it by the end of this week. Thank you for your patience!

[YuNong-Qiu]

Dear @axelalmet ,
Thank you for your answer. I will try it later. I am very interested in your research and look forward to your update!