plot_tsne_arrows: t-SNE plot with arrows

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

t-SNE plot with arrows

Description

Computes t-SNE into two dimensions and plots changes according to time. All the observations of a single subject are connected by an arrow ending at the last observation. In case there are missing values, PCA is performed using the nipals method of pcaMethods::pca, the method can be changed to "ppca" if nipals fails. CITATION: When using this function, cite the pcaMethods and Rtsne packages

Usage

plot_tsne_arrows(
  object,
  all_features = FALSE,
  center = TRUE,
  scale = "uv",
  perplexity = 30,
  pca_method = "nipals",
  color = group_col(object),
  time = time_col(object),
  subject = subject_col(object),
  alpha = 0.6,
  arrow_style = arrow(),
  title = "t-SNE changes",
  subtitle = paste("Perplexity:", perplexity),
  color_scale = getOption("notame.color_scale_dis"),
  text_base_size = 14,
  line_width = 0.5,
  ...
)

Arguments

object	a MetaboSet object
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
perplexity	the perplexity used in t-SNE
pca_method	the method used in PCA if there are missing values
color	character, name of the column used for coloring the points
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 Rtsne::Rtsne

Value

a ggplot object. If density is TRUE, the plot will consist of multiple parts and is harder to modify.

See Also

Rtsne

Examples

plot_tsne_arrows(drop_qcs(example_set), perplexity = 5)
# If the sample size is large, plot groups separately
plot_tsne_arrows(drop_qcs(example_set), perplexity = 5) +
  facet_wrap(~Group)

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