Hello,
I was using scanpy to cluster my data but i found the umap generated to not be comparable to the original umap library. Is there any way to debug this or get the same results on the UMAP library. Is there any additional normalization that scanpy does which I might be missing?
Are there more details you could provide?
For some initial pointers, you should already get comparable results with using umap.UMAP(...).fit_transform(adata.obsm["X_pca"]) and parameters used by sc.tl.umap() (some of them are also saved in adata.uns["umap"]["params"]).
I went through the documentation and saw the PCA being performed. This was the main factor.