ProjectUMAP- 3D projection lacks accuracy

[andynkili]

Dear developpers,

Thanks for the constant support and developing new tools to make single-cell data analysis easier.

I am trying to project query onto a reference using 3 UMAP components, instead of 2.
To assess the results, the current query is just a subset of the reference.
Essentially, I project query cells to the reference PCA space before projecting to UMAP (based on https://github.com/satijalab/seurat/issues/5199)
Here is the code:

library(plotly)
library(data.table)
options(future.globals.maxSize = 1000 * 1024^3)
set.seed(1234)
ref <- readRDS('SR.rds')
query = subset(ref, cells = sample(Cells(ref), 5000))


ref <- SCTransform(ref, variable.features.n = 3000, verbose = F)
ref <- RunPCA(ref, features=VariableFeatures(ref), npcs = 50, verbose = F)
ref <- FindNeighbors(ref, dims = 1:30, verbose = F)
ref <- RunUMAP(ref, dims = 1:30, n.components = 3,return.model = T)

  
set.seed(1234)
pca.features <- rownames(ref[['pca']]@feature.loadings)
query <- SCTransform(query,   residual.features = pca.features,  verbose = F)
#pca.feature have to match the features in query 'scale.data'
pca.features <- intersect(rownames(ref[['pca']]@feature.loadings),rownames(query@assays$SCT$scale.data))
query.pca.embeddings <- t(query@assays$SCT$scale.data[pca.features,]) %*% ref[['pca']]@feature.loadings[pca.features,]
query[['pca']] <- CreateDimReducObject(embeddings = query.pca.embeddings, key = "PC_", assay = "SCT"  )
query <- ProjectUMAP(query = query, query.reduction = "pca",
                     reference = ref, reference.reduction = "pca",
                     reduction.model = "umap", verbose=T)

Then I use plotly to visualize query and reference cells:

The picture is showing only NK.cells (reference is grey and query is dark greeen).
I don't understand the 2 cells in opposite coordinates. I was expecting the reference and query (subset of reference) to be more aligned.
And that effect is happening for every cell types: most of the query cells are grouped with corresponding ref cells in the 3D-UMAP but some query cells are far away from the reference.

Could you point me what am I missing there?

Best,
Andy