plot_tsne_hexbin: t-SNE hexbin plot
In antonvsdata/notame: Workflow for non-targeted LC-MS metabolic profiling

plot_tsne_hexbin

R Documentation

t-SNE hexbin plot

Description

Computes t-SNE into two dimensions and plots the map as hexagonal bins, where the value of the coloring variable is summarised for each bin, by default as the mean of the values inside the bin. In case there are missing values, PCA is performed using the nipals method of pcaMethods::pca, the method can be changed to "ppca" if niipals fails.

Usage

plot_tsne_hexbin(
  object,
  all_features = FALSE,
  center = TRUE,
  scale = "uv",
  pca_method = "nipals",
  perplexity = 30,
  fill = "Injection_order",
  summary_fun = "mean",
  bins = 10,
  title = "t-SNE",
  subtitle = paste("Perplexity:", perplexity),
  fill_scale = getOption("notame.fill_scale_con"),
  ...
)

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
`pca_method`	the method used in PCA if there are missing values
`perplexity`	the perplexity used in t-SNE
`fill`	character, name of the column used for coloring the hexagons
`summary_fun`	the function used to compute the value for each hexagon
`bins`	the number of bins in x and y axes
`title`, `subtitle`	the titles of the plot
`fill_scale`	the fill scale as returned by a ggplot function
`...`	additional arguments passed to Rtsne::Rtsne