specmine (version 4.0.0)

pca_pairs_kmeans_plot: PCA pairs plot with k-means clusters

Description

Creates a pairs plot of PCA scores coloured by k-means cluster assignment.

Usage

pca_pairs_kmeans_plot(
  dataset,
  pca.result,
  num.clusters = 3,
  kmeans.result = NULL,
  pcas = c(1, 2, 3, 4, 5)
)

Value

A ggmatrix object.

Arguments

dataset

Dataset used in the PCA.

pca.result

PCA result object.

num.clusters

Number of clusters.

kmeans.result

Optional precomputed k-means result.

pcas

Principal components to include.

Examples

# \donttest{
datamat <- matrix(
  rnorm(30),
  nrow = 6,
  dimnames = list(paste0("x", 1:6), paste0("s", 1:5))
)
metadata <- data.frame(class = factor(c("A", "A", "B", "B", "A")))
dataset <- list(data = datamat, metadata = metadata)
pca_res <- pca_analysis_dataset(dataset)
pca_pairs_kmeans_plot(dataset, pca_res, num.clusters = 2, pcas = 1:3)
# }