add_umap_embedding: run UMAP with 'uwot' and store the embedding model in...

In trichelab/velocessor: The world's dumbest single-cell RNA velocity calculator and loader

Description

run UMAP with uwot and store the embedding model in metadata(x)$uwot

Usage

add_umap_embedding(x, nc = 3L, ret = c("sce", "uwot"), rdn = NULL, ...)

Arguments

x	a SingleCellExperiment or a slice of one
nc	how many components to keep for uwot's UMAP embedding (3)
ret	return the modified "sce" (default) or "uwot" model? ("sce")
rdn	reducedDimName to use ("HARMONY" if present, "PCA" otherwise)
...	additional parameters for uwot::umap (e.g. y for SDR)

Value

 depending on `ret`, an embellished sce or a uwot model

See Also

uwot::umap

trichelab/velocessor documentation built on Jan. 5, 2022, 6:27 p.m.