I am totally new to Scanpy as I have been using Seurat so far.
I am trying to use Scanpy in conjunction with scVI to analyze some 10X data. The behavior to which I am used in Seurat is that the UMAP plot will look somewhat different depending on the number of PCs taken into analysis. In Scanpy, there is no option to set the number of PCs in sc.tl.umap, so I assume that the only parameter that matters is n_pcs in sc.pp.neighbors. However, setting this parameter to different values changes nothing for me. Does this make sense? Am I missing something?
Thank you in advance!