How to run fs.pp.construct_flows_from_cellphonedb

[OMIC-coding]

Hello, I noticed a function called construct_flows_from_cellphonedb that can be used as an alternative for construct_flows_from_cellchat when constructing signal flows. However, you haven't provided any explicit tutorials or explanation documents for me to understand what the parameters cellphonedb_output_key and cellphonedb_tfs_key should be to fit in this step.
Could you help me with that?

[OMIC-coding]

Maybe you can just upload some example files for this step, and I will make some attempts. From my perspective, constructing flows from cellphonedb is more compatible with the scanpy pipeline, so it would be more widely used than the original function in the tutorials.

[axelalmet]

Hi OMIC-coding,

Sorry for my very late response. You make a good point about 1) cellphonedb being more compatible with Scanpy (although LIANA's implementation of CellChat changes that), and 2) the functionality is there, so I should have some documentation for it.

I originally developed it during revisions but I should have an example. For your own example. Here's what I did:

1. For CellPhoneDB analysis, I used the "DEG-based method" as specified in the README, also known as Method 3 by the CellPhoneDB developers, e.g. via: https://github.com/ventolab/CellphoneDB/blob/master/notebooks/T1_Method3.ipynb.
   Run CellPhoneDB per condition that you are interested in.

An example script can be found at the FlowSigAnalysis_2023 repository here.

Let me know if you have any other questions. My plan is to include this properly as a tutorial in future FlowSig versions.

Best wishes,
Axel.