Run UMAP on a SingleCells object — umap

Wrapper around manifoldsR::umap() for the SingleCells class.

Usage

umap_sc(
  object,
  use_knn = TRUE,
  embd_to_use = "pca",
  no_embd_to_use = NULL,
  n_dim = 2L,
  k = 15L,
  min_dist = 0.5,
  spread = 1,
  knn_method = c("hnsw", "balltree", "annoy", "nndescent", "exhaustive"),
  nn_params = manifoldsR::params_nn(),
  umap_params = manifoldsR::params_umap(),
  seed = 42L,
  .verbose = TRUE
)

Arguments

object: SingleCells class.
use_knn: Boolean. Use the kNN graph found in the object. Defaults to TRUE. If not available, will default to the embedding.
embd_to_use: String. The embedding to use for UMAP. Must be available in the object.
no_embd_to_use: Optional integer. Number of embedding dimensions to use. If NULL all will be used.
n_dim: Integer. Number of UMAP dimensions. Defaults to 2L.
k: Integer. Number of nearest neighbours. Defaults to 15L.
min_dist: Numeric. Minimum distance between embedded points. Defaults to 0.5.
spread: Numeric. Effective scale of embedded points. Defaults to 1.0.
knn_method: String. Approximate nearest neighbour algorithm. One of "hnsw", "balltree", "annoy", "nndescent", or "exhaustive".
nn_params: Named list. See manifoldsR::params_nn().
umap_params: Named list. See manifoldsR::params_umap().
seed: Integer. For reproducibility.
.verbose: Boolean. Controls verbosity.

Value

The object with a "umap" embedding added.