How to construct the flow expression matrices?

[yixudong]

Dear Axel,
After The error(#6), I'm sorry I ran into the error again on the next run:

Whether this is caused by The cell-cell communication inference.csv?
I used Cellchat.object@net$prob as my inference.csv, lt look at :

We would very much appreciate your help!
Best wishes,
Yixudong.

[axelalmet]

Hi Yixudong,

You're right, the issue is that FlowSig doesn't work with the direct probability matrices created by CellChat. To run FlowSig with CellChat analysis, I would generate the interaction data.frame using CellChat's subsetCommunication() method, as specified under the section of "Extract the inferred cellular communication network as a data frame" in the CellChat tutorial.

That is, you should then create df.net <- subsetCommunication(cellchat) and then save df.net as inference.csv.

Hope that helps!

[yixudong]

Hi Axel, it worked, but when i run fs.pp.determine_differentially_flowing_vars(), it emerge a new error :

Traceback (most recent call last):
File "", line 1, in
AttributeError: module 'flowsig.preprocessing' has no attribute 'determine_differentially_flowing_vars' . I just updated figslow and his version is 0.1.1

[axelalmet]

Hi yixudong,

That's a mistake on my behalf. I'm very sorry about that! Try updating to 0.1.2 and going back to running:

fs.pp.determine_informative_variables(adata,  
                                    flowsig_expr_key = 'X_flow',
                                    flowsig_network_key = 'flowsig_network',
                                    spatial = False,
                                    condition_key = condition_key,
                                    control_key =  'Ctrl',
                                    qval_threshold = 0.05,
                                    logfc_threshold = 0.5)

The reason this is an error is that determine_differentially_flowing_vars is supposed to be an internal function that determine_informative_variables calls. I had mixed them up when revisiting the code.

Sorry again!

[wolfQK]

Change the second line of flowsig/flowsig/preprocessing/init.py to:
from ._flow_preprocessing import subset_for_flow_type, filter_flow_vars, determine_differentially_flowing_vars, determine_spatially_flowing_vars, determine_informative_variables
This modification should resolve the issue. @axelalmet