update a SingleCellExperiment with UMAP reductions of embeddings produced with PyTorch-BigGraph

update a SingleCellExperiment with UMAP reductions of embeddings produced with PyTorch-BigGraph

umap_CG(trout, sce, ncomp = 3, ...)

Arguments

trout

output of `BiocPBG::train_eval`

sce

SingleCellExperiment instance derived from or consistent with the one from which `trout` was produced

ncomp

numeric(1) passed as `n_components` to `uwot::umap`

...

named arguments other than `n` to be passed to `uwot::umap`

Value

The `sce` is updated to include a `reducedDim` component named `UMAP` based on the cell embedding, and the rowData component is updated to include the UMAP applied to gene embedding