cannot reproduce harmony processing output about harmony

[ilyakorsunsky]

Dear @JuHey,

During the revisions, we decided to add a PCA-preprocessing step as the default behavior of HarmonyMatrix. Thus, the 2020 version you posted above re-PCA'd the input PCs. To get the original behavior back, please specify do_pca=FALSE:

hem <- HarmonyMatrix(pca, batch, theta=4, do_pca=FALSE)

I'll also add that in this example, there are sources of batch from both donor and study. With Harmony, you can model and remove both for a more thorough integration.

Finally, if you want to run Harmony in Python, you can now do it directly with @slowkow's harmonypy package (https://github.com/slowkow/harmonypy).

Thanks for pointing out this behavior!

Best,
Ilya

[JuHey]

Thank you very much @ilyakorsunsky !!!