Allow usage of other embeddings

Teichlab / bbknn

Batch balanced KNN

MIT License

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Allow usage of other embeddings #20

Closed dawe closed 4 years ago

dawe commented 4 years ago

I wanted to build bbknn graph starting from a different embedding than X_pca. I've added the use_rep option, which is consistent with Scanpy's sc.pp.neighbors option.

ktpolanski commented 4 years ago

Huh, I remember this crossing my mind before but I never actually carried it out. I'll sort it out soon and release a new version. Thanks for the reminder.

ktpolanski commented 4 years ago

I added the use_rep argument, but handled it slightly differently (no defaulting to PCA, amending the original PCA check so that BBKNN doesn't abort if there's no PCA regardless of what was chosen). Released as 1.3.7, should be good to go. Thanks for the reminder again.