Strong impact of number of ADT PCs on WNN UMAP?

[erflynn]

I'm running WNN following the tutorial on a dataset of about 200,000 skin cells. I noticed that choice of number of ADT PCs has a huge impact on the UMAP -- the UMAP clearly looks better with more ADT PCs, despite the elbow plot indicating we should likely use fewer. I am using the same exact settings (30 RNA PCs) except the number of ADT PCs. Seurat version 4.3.0.

wnn <- FindMultiModalNeighbors(
  wnn, reduction.list = list("pca", "apca"), 
  dims.list = list(1:30, 1:n_adt_pcs), modality.weight.name = "RNA.weight",
  prune.snn=1/20 # adjusted to avoid small clusters
)
wnn <-RunUMAP(wnn, nn.name = "weighted.nn", reduction.name = "wnn.umap", reduction.key = "wnnUMAP_")

Have you noticed this before? Is this expected behavior? What would you recommend doing to proceed?