specmine (version 4.0.0)

tsne_pairs_plot: t-SNE pairs plot

Description

Creates a pairs plot for selected t-SNE dimensions.

Usage

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

Value

A GGally pairs plot object.

Arguments

dataset

Dataset used to calculate the embedding.

tsne.result

Result returned by tsne_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

if (requireNamespace("Rtsne", 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))
    )
  )

  tsne.result <- tsne_analysis_dataset(
    dataset,
    n_components = 3,
    perplexity = 2,
    max_iter = 250,
    seed = 42
  )

  tsne_pairs_plot(
    dataset,
    tsne.result,
    column.class = "class",
    dims = 1:3
  )
}