Setup UMAP parameters.

Usage

setup_UMAP(
  k = 2L,
  n_neighbors = 15L,
  init = "spectral",
  metric = c("euclidean", "cosine", "manhattan", "hamming", "categorical"),
  n_epochs = NULL,
  learning_rate = 1,
  scale = TRUE
)

Arguments

k: Integer: Number of components.
n_neighbors: Integer: Number of keighbors.
init: Character: Initialization type. See uwot::umap "init".
metric: Character: Distance metric to use: "euclidean", "cosine", "manhattan", "hamming", "categorical".
n_epochs: Integer: Number of epochs.
learning_rate: Float: Learning rate.
scale: Logical: If TRUE, scale input data before doing UMAP.

Value

UMAPParameters object.

Details

A high n_neighbors value may give error in some systems: "Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : function 'as_cholmod_sparse' not provided by package 'Matrix'"

Author

EDG