I have been getting a bit confused as to which embeddings should be used to calculate neighbours and moments for scvelo. In short, I have 4 samples that have been library prep batch-corrected and harmonized with scVI. I then used palantir to generate diffusion maps (standard and multiscale) without MAGIC imputation, and I then drew UMAPs, TSNE and FA graphs using those embeddings.
When proceeding with scVelo, I am a bit confused whether I should supply scVI embeddings as they are corrected. I am also wondering if supplying any of the diffusion map embeddings would be a valid choice.
Finally, if I further decide to subset the data (e.g. leaving only half of the cell types for analysis), what kind of embeddings can I supply again since I assume the scVI ones would need to be recomputed somehow?
Please advise, if possible. Thank you for any help!