PLS-DA Plot — plot_plsda • glyvis

Draw a PLS-DA scores plot. Currently supported data types:

glystats_plsda_res: Result from glystats::gly_plsda().
glyexp_experiment: Experiment created by glyexp::experiment(). PLS-DA analysis is first performed using glystats::gly_plsda(), then the result is plotted.

Usage

plot_plsda(x, type = "scores", groups = NULL, group_col = NULL, ...)

# S3 method for class 'glystats_plsda_res'
plot_plsda(x, type = "scores", groups = NULL, group_col = NULL, ...)

# S3 method for class 'glyexp_experiment'
plot_plsda(
  x,
  type = "scores",
  groups = NULL,
  group_col = NULL,
  stats_args = list(),
  ...
)

Arguments

x: An object to be plotted.
type: The type of plot, one of "loadings", "scores", "vip", or "variance". Defaults to "scores".
groups: A factor or character vector specifying group membership for each sample. If provided, the plot will be colored by group. Only applicable to "scores" and "loadings" types.
group_col: A character string specifying where to find the group information. If you uses glystats::gly_plsda() on a glyexp::experiment() to get the result, sample information has already been added to the result. In this case, you can specify the column name in the sample information tibble to be used for coloring. If not provided, this function will try "group".
...: Ignored.
stats_args: A list of keyword arguments to pass to glystats::gly_plsda().

Value

A ggplot object.