specmine (version 4.0.0)

umap_pairs_kmeans_plot: UMAP pairs k-means plot

Description

Creates a pairs plot for UMAP dimensions coloured by k-means clusters.

Usage

umap_pairs_kmeans_plot(
  dataset,
  umap.result,
  num.clusters = 3,
  kmeans.result = NULL,
  dims = 1:min(5, ncol(umap.result$embedding))
)

Value

A GGally pairs plot object.

Arguments

dataset

Dataset to cluster.

umap.result

Result returned by umap_analysis_dataset().

num.clusters

Number of k-means clusters.

kmeans.result

Optional result returned by clustering().

dims

Embedding dimensions to include in the pairs plot.

Examples

if (requireNamespace("uwot", quietly = TRUE) &&
    requireNamespace("GGally", quietly = TRUE)) {
  datamat <- matrix(
    rnorm(40),
    nrow = 5,
    dimnames = list(
      paste0("x", 1:5),
      paste0("s", 1:8)
    )
  )

  dataset <- list(
    data = datamat,
    metadata = data.frame(
      class = factor(rep(c("A", "B"), length.out = 8))
    )
  )

  umap.result <- umap_analysis_dataset(
    dataset,
    n_components = 3,
    n_neighbors = 3,
    seed = 42
  )

  umap_pairs_kmeans_plot(
    dataset,
    umap.result,
    num.clusters = 2,
    dims = 1:3
  )
}