Comments (2)
jlmelville
commented on June 8, 2024
Unfortunately, I don't know anything about seurat, so I don't know what the seurat@reductions$umap object is. Is it the output coordinates of running UMAP on your RNA data (presumably a 2D matrix)? If so, that's not enough information for umap_transform. You need the object returned from running uwot::umap(ret_model = TRUE). But I don't think mixing low-level uwot functions with higher-level seurat data is a good way forward, when clearly neither of us know much about how seurat's internals interact with uwot.
I wish I could be more helpful but I would recommend going to the seurat repo and asking how to transform new data. A similar error message was reported at satijalab/seurat#7378 -- maybe following the responses there can help?
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