plot_tsne: t-SNE scatter plot

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

t-SNE scatter plot

Description

Computes t-SNE into two dimensions and plots the map points. 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(
  object,
  all_features = FALSE,
  center = TRUE,
  scale = "uv",
  perplexity = 30,
  pca_method = "nipals",
  color = group_col(object),
  shape = color,
  label = NULL,
  density = FALSE,
  title = "t-SNE",
  subtitle = paste("Perplexity:", perplexity),
  color_scale = NA,
  shape_scale = getOption("notame.shape_scale"),
  fill_scale = getOption("notame.fill_scale_dis"),
  text_base_size = 14,
  point_size = 2,
  ...
)

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. Set to NULL for black color.
shape	character, name of the column used for shape. Set to NULL for uniform round shapes.
label	character, name of the column used for point labels
density	logical, whether to include density plots to both axes. The density curves will be split and colored by the 'color' variable.
title, subtitle	the titles of the plot
color_scale	the color scale as returned by a ggplot function. Set to NA to choose the appropriate scale based on the class of the coloring variable.
shape_scale	the shape scale as returned by a ggplot function
fill_scale	the fill scale used for density curves. If a continuous variable is used as color, density curve will be colorless.
text_base_size	numeric, base size for text
point_size	numeric, size of the points
...	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(merged_sample, color = "Time", shape = "Group")

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