specmine (version 4.0.0)

umap_pairs_plot: UMAP pairs plot

Description

Creates a pairs plot for selected UMAP dimensions.

Usage

umap_pairs_plot(
  dataset,
  umap.result,
  column.class = NULL,
  dims = 1:min(5, ncol(umap.result$embedding)),
  ...
)

Value

A GGally pairs plot object.

Arguments

dataset

Dataset used to calculate the embedding.

umap.result

Result returned by umap_analysis_dataset().

column.class

Optional metadata column used to colour samples.

dims

Embedding dimensions to include in the pairs plot.

...

Additional arguments passed to GGally::ggpairs().

Examples

# \donttest{
if (requireNamespace("uwot", quietly = TRUE) &&
    requireNamespace("GGally", quietly = TRUE)) {
  datamat <- matrix(rnorm(40), nrow = 5)
  dataset <- list(
    data = datamat,
    metadata = data.frame(
      class = factor(rep(c("A", "B"), length.out = 8))
    )
  )
  result <- umap_analysis_dataset(
    dataset,
    n_components = 3,
    n_neighbors = 3
  )
  umap_pairs_plot(
    dataset,
    result,
    column.class = "class",
    dims = 1:3
  )
}
# }