Phate using harmony reduction

[wiktormiko]

Hi, I was wondering if I could use Phate with harmony corrected PC's. Is there a way to skip calculating PCA while running PHATE and use pre-computed Harmony embeddings instead?

[nishuang83]

Yes, you can set n_pca to None and input your precomputed embeddings.

phate_op = phate.PHATE(n_pca=None)
phate_op.fit_transform(your_embeddings)