getDimRedPlot: getDimRedPlot

In demuellae/muRtools: Mueller's R tools

getDimRedPlot

Description

Generate a plot from dimension reduction coordinates

Usage

getDimRedPlot(
  coords,
  annot = NULL,
  colorCol = NULL,
  shapeCol = NULL,
  colScheme = "[auto]",
  ptSize = 3,
  addLabels = FALSE,
  addDensity = FALSE,
  addVoronoi = FALSE,
  annot.text = NULL,
  orderCol = NULL,
  facetCols = NULL
)

Arguments

coords	dimension reduction coordinates
annot	annotation matrix with the same number of rows as coord
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. can be a character vector with the supplied colors. Alternatively, if it is a one-element character vector "[auto]" the color scheme will be selected automatically using muRtools::ggAutoColorScale. If NULL, ggplots default color scheme will be used.
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
addVoronoi	should a Voronoi tessalation grid (based on colorCol) be added to the plot
annot.text	optional text to be added in the lower right corner of the plot
orderCol	name or index in the annotation matrix (annot) that should be used for ordering the points. If not NULL Points will be ordered increasingly by their value, i.e. higher-valued points are plottet over lower-valued points
facetCols	name (string) of columns to be used for faceting the resulting plot. Each facet will contain all the points not in the facet as grey points.

Value

a ggplot2 object containing the dimension reduction plot

Author(s)

Fabian Mueller

Examples

df <- data.frame(
	x = c(rnorm(20, mean=0, sd=0.2), rnorm(10, mean=1, sd=0.4), rnorm(15, mean=1, sd=0.2)),
	y = c(rnorm(20, mean=0, sd=0.2), rnorm(10, mean=1, sd=0.4), rnorm(15, mean=0.5, sd=0.3)),
	group = rep(c("group1", "group2", "group3"), times=c(20,10,15)),
	stringsAsFactors=FALSE
)
getDimRedPlot(df[,c("x", "y")], annot=df[,c("group"), drop=FALSE], colorCol="group")
getDimRedPlot(df[,c("x", "y")], annot=df[,c("group"), drop=FALSE], colorCol="group", addDensity=TRUE)

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