plot_pca_arrows: PCA plot with arrows

In antonvsdata/notame: Workflow for non-targeted LC-MS metabolic profiling

PCA plot with arrows

Description

Plots changes in PCA space according to time. All the observations of a single subject are connected by an arrow ending at the last observation.

Usage

plot_pca_arrows(
  object,
  pcs = c(1, 2),
  all_features = FALSE,
  center = TRUE,
  scale = "uv",
  color = group_col(object),
  time = time_col(object),
  subject = subject_col(object),
  alpha = 0.6,
  arrow_style = arrow(),
  title = "PCA changes",
  subtitle = NULL,
  color_scale = getOption("notame.color_scale_dis"),
  text_base_size = 14,
  line_width = 0.5,
  ...
)

Arguments

object	a MetaboSet object
pcs	numeric vector of length 2, the principal components to plot
all_features	logical, should all features be used? If FALSE (the default), flagged features are removed before visualization.
center	logical, should the data be centered prior to PCA? (usually yes)
scale	scaling used, as in pcaMethods::prep. Default is "uv" for unit variance
color	character, name of the column used for coloring the arrows
time	character, name of the column containing timepoints
subject	character, name of the column containing subject identifiers
alpha	numeric, value for the alpha parameter of the arrows (transparency)
arrow_style	a description of arrow heads, the size and angle can be modified, see ?arrow
title, subtitle	the titles of the plot
color_scale	the color scale as returned by a ggplot function
text_base_size	the base size of the text
line_width	the width of the arrows
...	additional arguments passed to pcaMethods::pca

Value

a ggplot object.

See Also

pca

Examples

plot_pca_arrows(drop_qcs(example_set))
# If the sample size is large, plot groups separately
plot_pca_arrows(drop_qcs(example_set)) +
  facet_wrap(~Group)

antonvsdata/notame documentation built on Sept. 14, 2024, 11:09 p.m.