Run UMAP on samples

Usage

reduce_umap(
  x,
  experiment,
  assay,
  features = NULL,
  top_n = NULL,
  neighbors = NULL,
  components = 2,
  metric = "euclidean",
  min_distance = 0.01,
  seed = 1,
  ...
)

Arguments

x: A MultiAssayExperiment object.
experiment: Optional experiment name.
assay: Assay name or one-based assay index.
features: Optional feature subset.
top_n: Optional number of most variable features to retain.
neighbors: Number of nearest neighbors. When NULL, uses the smaller of 15 and the number of samples minus one.
components: Embedding dimensions.
metric: Distance metric.
min_distance: Minimum embedding distance.
seed: Optional random seed.
...: Additional arguments passed to uwot::umap().

Value

The native sample-by-component matrix returned by uwot.