pca_pairs_kmeans_plot: PCA pairs plot with k-means clusters

In specmine: Metabolomics and Spectral Data Analysis and Mining

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)
)

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.

Value

A ggmatrix object.

Examples

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)

specmine documentation built on Aug. 5, 2026, 5:06 p.m.