Principal component analysis of a RiboClass object

Usage

plot_pca(
  ribo,
  color_col = NULL,
  axes = c(1, 2),
  only_annotated = FALSE,
  title = "default",
  subtitle = "samples",
  object_only = FALSE
)

Arguments

ribo: A RiboClass object.
color_col: Name of the column in the metadata used for coloring samples.
axes: Two-element vector indicating which pair of principal components to show.
only_annotated: If TRUE, use only annotated sites to plot PCA.
title: Title to display on the plot. 'default' for default title.
subtitle: Subtitle to display on the plot. 'samples' for number of samples. 'none' for no subtitle.
object_only: Return directly the full dudi.pca object, without generating the plot.

Value

A ggplot or a dudi.pca object if object_only is set to True.

Examples

data('ribo_toy')
plot_pca(ribo_toy,'run')