plotPCA {affycoretools} | R Documentation |
This function makes a PCA plot from an ExpressionSet, exprSet or matrix
plotPCA(eset, 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, ...)
eset |
An ExpressionSet , exprSet 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 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 |
... |
Further arguments to be passed to plot . See the help page
for plot for further information. |
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>