re variable genes used does not match

[haircell]

Hi,

I'm having some trouble with the variable genes selection for the RunSWNE Seurat wrapper function. I have my integrated data Seurat object and I follow the steps outlined here: https://yanwu2014.github.io/swne/Examples/multiple_pancreas_alignment_swne.html

However, when running the RunSWNE() command to create the swne.embeddings, instead of [1] "2000 variable genes to use", I see [1] "15760 variable genes to use" in the Console. This is the total number of genes in the dataset, not just the variable genes. Even when I specifically set genes.use <- VariableFeatures(obj), I get the same read in the Console (i.e. all genes are being used). I noticed that the pancreas_integrated_seurat.Robj object in the vignette is already subseted to only the 2000 most variable genes. I'm wondering if the Console is printing the total number of genes in the dataset or if it's actually using all genes and not just the variable ones?

Thanks!