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Grouped embedding scatter

Source: R/embedding.R
plot_embedding.Rd

Plot samples in a two-dimensional embedding, coloured by group. The embedding can be supplied already computed, or computed here from a feature matrix with stats::prcomp(), Rtsne, or umap.

Usage

plot_embedding(
  data,
  groups,
  method = c("pca", "tsne", "umap", "none"),
  perplexity = 30,
  seed = NULL,
  ellipse = FALSE,
  label_centres = FALSE,
  palette = "house",
  title = NULL,
  xlab = NULL,
  ylab = NULL,
  font = "Arial"
)

Arguments

data

A feature matrix with samples in rows, or a two-column matrix of coordinates when method = "none".

groups

Group labels, one per sample.

method

Embedding to compute: "pca", "tsne", "umap", or "none" when data already holds coordinates.

perplexity

Perplexity for t-SNE. Values much larger than the number of samples are rejected by the back end.

seed

Optional seed for the stochastic embeddings.

ellipse

Draw a confidence ellipse per group.

label_centres

Label each group at the centre of its points.

palette

Palette name passed to get_color().

title, xlab, ylab

Axis and plot labels.

font

Font family used in the plot.

Value

A ggplot object.

Details

plot_PCA() and plot_UMAP() are thin wrappers around this function, so a figure keeps the same look whichever embedding it shows.

See also

plot_PCA(), plot_UMAP()

Examples

set.seed(1)
data <- matrix(rnorm(200), nrow = 20)
groups <- rep(c("A", "B"), each = 10)
p <- plot_embedding(data, groups, method = "pca")