Comments (1)
Hi, my understanding is that you downloaded a reference dataset and want your test dataset to have a similar UMAP embedding. UMAP is not a part of scVI-tools. Therefore this is not a bug. Please use our discourse forum for feature requests. You might want to look into https://umap-learn.readthedocs.io/en/latest/transform.html to compute the same UMAP for reference and query data, but there is no way to yield this from an h5ad with an existing UMAP.
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