Open sinnamone opened 5 years ago
I think your question relates to setting the random seed in order to get the results although the computation is stochastic. There is an issue related to this https://github.com/jacoblevine/PhenoGraph/issues/14. The Louvain code is in C so it is useless to set a random seed in the Python code calling the Louvain implementation. The seed must be pass to the C code. If you have programming skill you could try to implement it. What you observe so far is natural and still inform you about the robustness/power of your data in order to aggregate themselves in clusters. Best
We have implemented a random seed selection in the most recent histoCAT version. Here is the detailed commit: https://github.com/BodenmillerGroup/histoCAT/commit/8d74a318764e83408b648a61465c5140749ca835
Otherwise, feel free to use the histoCAT Phenograph version.
Best
Denis
Dear @SamGG and @DenisSch thank you for the suggestion,
I was able to fix seed using the file "community" present in histoCAT tool, parsing core.py and install again phenograph. I tested these changes first on my mac with good results, now I'm testing the same changes on the unix server but I noticed that the file in histoCAT/histoCAT/3rdParty/PhenoGraph/Louvain_d/community doesn't have the -s flag.
I wonder if it is possible to fix the seed also on linux server or only on mac operating systems?
Best regards,
Simone
I have create a new issue for that on the histoCAT repository. I will do my best to include it into the next update.
I ran into the same problem.
Here is a link to a fork of the Phenograph repo (DeterministicPhenoGraph), where you can set a seed for the Louvain. This should work on all platforms and allows you to get reproducible results.
Hi,
I ran Phenograph 4 times using the same input matrix and I have noted that the results is different in term of output number of cluster.
How I can set the parameters for reproduce (or modify the seed) the clustering results of Phenograph (or to have at list a similar results)?