ggbiplot: Biplot for Principal Components using ggplot2

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Description

Biplot for Principal Components using ggplot2

Usage

ggbiplot(
  pcobj,
  choices = 1:2,
  scale = 1,
  pc.biplot = TRUE,
  obs.scale = 1 - scale,
  var.scale = scale,
  groups = NULL,
  ellipse = FALSE,
  ellipse.prob = 0.68,
  labels = NULL,
  labels.size = 3,
  alpha = 1,
  var.axes = TRUE,
  circle = FALSE,
  circle.prob = 0.69,
  varname.size = 3,
  varname.adjust = 1.5,
  varname.abbrev = FALSE
)

Arguments

pcobj	an object returned by prcomp() or princomp()
choices	which PCs to plot
scale	covariance biplot (scale = 1), form biplot (scale = 0). When scale = 1, the inner product between the variables approximates the covariance and the distance between the points approximates the Mahalanobis distance.
pc.biplot	for compatibility with biplot.princomp()
obs.scale	scale factor to apply to observations
var.scale	scale factor to apply to variables
groups	optional factor variable indicating the groups that the observations belong to. If provided the points will be colored according to groups
ellipse	draw a normal data ellipse for each group?
ellipse.prob	size of the ellipse in Normal probability
labels	optional vector of labels for the observations
labels.size	size of the text used for the labels
alpha	alpha transparency value for the points (0 = transparent, 1 = opaque)
var.axes	draw arrows for the variables?
circle	draw a correlation circle? (only applies when prcomp was called with scale = TRUE and when var.scale = 1)
circle.prob	definition of circle.prob
varname.size	size of the text for variable names
varname.adjust	adjustment factor the placement of the variable names, >= 1 means farther from the arrow
varname.abbrev	whether or not to abbreviate the variable names

Value

A ggplot2 plot

Author(s)

Vincent Q. Vu.

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.