PhenoGraph does not accept seed

[DenisSch]

As reported by several users PhenoGraph does not accept the seed from Matlab. @votti @JanaFischer any ideas for a work around?

[votti]

Hi,
The 'issue' is that currently HistoCAT is calling the louvain clustering via a systems call:
https://github.com/BodenmillerGroup/histoCAT/blob/6ad66331387a3afd4841ce6299402add8bfdf3f0/histoCAT/3rdParty/PhenoGraph/LouvainfromBin.m#L28

That means the matlab random seed will not affect this call.
The Louvain c++ code is random due to the following line:
https://github.com/BodenmillerGroup/histoCAT/blob/6ad66331387a3afd4841ce6299402add8bfdf3f0/histoCAT/3rdParty/PhenoGraph/Louvain_d/community.cpp#L278

Which is used in the command line call:
https://github.com/BodenmillerGroup/histoCAT/blob/6ad66331387a3afd4841ce6299402add8bfdf3f0/histoCAT/3rdParty/PhenoGraph/Louvain_d/main_community.cpp#L141

Currently, already a random seed is set as a function of time & process id in the main command line program:
https://github.com/BodenmillerGroup/histoCAT/blob/bb14e391ce98ae61aaf22df0f055a4df9990b78a/histoCAT/3rdParty/PhenoGraph/Louvain_d/main_community.cpp#L115

My suggestion would be to add a command line argument random_seed to the main_community.cpp and use this instead as a seed, if provided.