plotPCA {affycoretools} | R Documentation |
This function makes a PCA plot from an exprSet
plotPCA(eset, groups, groupnames, addtext = NULL, x.coord = NULL, y.coord = NULL, screeplot = FALSE, squarepca = FALSE)
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 |
This function returns nothing. It is called only for the side effect of producing a PCA plot or screeplot.
James W. MacDonald <jmacdon@med.umich.edu>