UMAP Embedding of Spectral Data

Computes a UMAP (Uniform Manifold Approximation and Projection) embedding of the spectral data. Requires the uwot package.

Usage

hs_umap(
  cube,
  n_components = 2L,
  n_neighbors = 15L,
  min_dist = 0.1,
  pca_pre = 20L
)

Arguments

cube

An hsi_cube object.

n_components

Integer. UMAP dimensions. Default 2.

n_neighbors

Integer. Default 15.

min_dist

Numeric. Default 0.1.

pca_pre

Integer or NULL. PCA pre-reduction dimensionality. Default 20.

Value

A list with class "hsi_umap" containing embedding matrix and spatial coordinates.

Examples

# \donttest{
# Requires uwot package
cube <- hs_example_cube()
if (requireNamespace("uwot", quietly = TRUE)) {
  umap_result <- hs_umap(cube, n_components = 2)
}
# }