plotDimRed: getDimRedPlot

In demuellae/muRtools: Mueller's R tools

getDimRedPlot

Description

Generate a plot from a feature matrix

Usage

plotDimRed(
  X,
  dimRedFun = getDimRedCoords.pca,
  annot = NULL,
  colorCol = NULL,
  shapeCol = NULL,
  colScheme = NULL,
  ptSize = 3,
  addLabels = FALSE,
  addDensity = FALSE,
  annot.text = NULL,
  ...
)

Arguments

X	feature matrix containing one row for each observation and one column for each feature
dimRedFun	function to do dimension reduction. E.g. getDimRedCoords.pca, getDimRedCoords.mds, getDimRedCoords.tsne,
annot	annotation matrix with the same number of rows as X
colorCol	name or index in the annotation matrix (annot) that should be used for coloring the points if colorCol not supplied but annot is supplied, it defaults to the first annotation column
shapeCol	name or index in the annotation matrix (annot) that should be used for point shapes if shapeCol not supplied but annot is supplied and has more than one column, it defaults to the second annotation column
colScheme	color sheme to be used in coloring the points
ptSize	size of the points in the scatterplot
addLabels	should observation labels be added to each point
addDensity	should Gaussian Kernel density estimation be performed and the contour lines plotted for each color group
annot.text	optional text to be added in the lower right corner of the plot
...	arguments to be passed on to dimRedFun

Value

a ggplot2 object containing the dimension reduction plot

Author(s)

Fabian Mueller

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