Hello ! I’m new here so not sure if i’m doing this correctly but here we go. I’m building a pipeline to deal with anndata objects (for analysis, visualization etc.)
The input of my pipeline is actually the output of an encoder, of a VAE. Therefore, I already reduced the dimensions of my dataset.
Once i’ve created an anndata object with the encoder’s output I want to use sc.pp.neighbors but without applying any kind of dimensionality reduction’s step. To do so, i’m using adata.X as use_rep but I’m wondering about the parameter method = umap. Is this method going to ‘transform’ my ‘raw’ datas ?
Documentation says it’s an optional parameter but i’m not sure of what sc.pp.neighbors is doing without the method parameter.
Also, to be able to run metrics such as Silhouette score, I needed an embedding to be store in adata.obsm. And in the same purpose of not computing any other dimensionality reduction step, I wrote this : adata.obsm[‘embeddings’] = adata.X
Does it make any sense ? Like this I wanted to make sure that everything is computed on the input datas far away from PCA / UMAP etc.
Thank you !