plotAllDimRed: plotAllDimRed

In demuellae/muRtools: Mueller's R tools

plotAllDimRed

Description

Generate a plots with multiple methods and parameter settings from a feature matrix

Usage

plotAllDimRed(
  X,
  fn.prefix = NULL,
  fn.suffix = "",
  annot = NULL,
  distMethods = c(euc = "euclidean", man = "manhattan"),
  width = 10,
  height = 10,
  ...
)

Arguments

X	feature matrix containing one row for each observation and one column for each feature
fn.prefix	file prefix to be used for the resulting plots. If NULL, no plot is actually created, but a list of resulting plot objects is returned
fn.suffix	file suffix to be used for the resulting plots
annot	annotation matrix with the same number of rows as X
distMethods	distance methods for MDS and t-SNE
width	width of the resulting plot
height	height of the resulting plot
...	arguments to be passed on to getDimRedPlot

Details

Currently, PCA, MDS and t-SNE are employed by default with euclidean and manhattan distance metrics where applicable

Value

(invisibly) a list of lists containing the created plots as ggplot objects and additional info for each plot

Author(s)

Fabian Mueller

demuellae/muRtools documentation built on Sept. 8, 2023, 4:32 p.m.