plotPCA {affycoretools}R Documentation

A Function to Make a PCA Plot from an exprSet

Description

This function makes a PCA plot from an exprSet

Usage

plotPCA(eset, groups, groupnames, addtext = NULL, x.coord = NULL,
y.coord = NULL, screeplot = FALSE, squarepca = FALSE)

Arguments

eset An exprSet
groups A numeric vector delineating group membership for samples.
groupnames A character vector describing the different groups.
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

Value

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

Author(s)

James W. MacDonald <jmacdon@med.umich.edu>


[Package affycoretools version 1.4.0 Index]