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It's an interesting question. At the moment, that is not possible (version 0.2.0).
Python package umap-learn has support for supervised and semi-supervised embedding. It should be possible to port that functionality to the R package. both into the method="umap-learn" wrapper and the method="naive" implementation. Unfortunately, I can't give an estimate or timeline for that now.
Is it possible to provide this implementation of UMAP label information (even partial labeling) to help guide the embedding?
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