plotPCA: A Function to Make a PCA Plot from an ExpressionSet or matrix

In affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Description

This function makes a PCA plot from an ExpressionSet or matrix

Usage

## S4 method for signature 'matrix'
plotPCA(
  object,
  groups = NULL,
  groupnames = NULL,
  addtext = NULL,
  x.coord = NULL,
  y.coord = NULL,
  screeplot = FALSE,
  squarepca = FALSE,
  pch = NULL,
  col = NULL,
  pcs = c(1, 2),
  legend = TRUE,
  main = "Principal Components Plot",
  plot3d = FALSE,
  outside = FALSE,
  ...
)

## S4 method for signature 'ExpressionSet'
plotPCA(object, ...)

Arguments

object	An ExpressionSet object or matrix.
groups	A numeric vector delineating group membership for samples. Default is NULL, in which case default plotting symbols and colors will be used.
groupnames	A character vector describing the different groups. Default is NULL, in which case the sample names will be used.
addtext	A character vector of additional text to be placed just above the plotting symbol for each sample. This is helpful if there are a lot of samples for identifying e.g., outliers.
x.coord	Pass an x-coordinate if automatic legend placement fails
y.coord	Pass a y-coordinate if automatic legend placement fails.
screeplot	Boolean: Plot a screeplot instead of a PCA plot? Defaults to FALSE.
squarepca	Should the y-axis of the PCA plot be made comparable to the x-axis? This may aid in interpretation of the PCA plot. Defaults to FALSE.
pch	A numeric vector indicating what plotting symbols to use. Default is NULL, in which case default plotting symbols will be used. Note that this argument will override the 'groups' argument.
col	A numeric or character vector indicating what color(s) to use for the plotting symbols. Default is NULL in which case default colors will be used. Note that this argument will override the 'groups' argument.
pcs	A character vector of length two (or three if plot3d is TRUE), indicating which principal components to plot. Defaults to the first two principal components.
legend	Boolean. Should a legend be added to the plot? Defaults to TRUE.
main	A character vector for the plot title.
plot3d	Boolean. If TRUE, then the PCA plot will be rendered in 3D using the rgl package. Defaults to FALSE. Note that the pcs argument should have a length of three in this case.
outside	Boolean. If TRUE the legend will be placed outside the plotting region, at the top right of the plot.
...	Further arguments to be passed to plot. See the help page for plot for further information.

Value

This function returns nothing. It is called only for the side effect of producing a PCA plot or screeplot.

Functions

• plotPCA,ExpressionSet-method:

Author(s)

James W. MacDonald <[e-mail]>

Examples

library("affy")
data(sample.ExpressionSet)
plotPCA(sample.ExpressionSet, groups =
 as.numeric(pData(sample.ExpressionSet)[,2]), groupnames =
 levels(pData(sample.ExpressionSet)[,2]))

affycoretools documentation built on Nov. 8, 2020, 6 p.m.