plotPCA | R Documentation |
This function makes a PCA plot from an ExpressionSet or matrix
## 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, ...)
object |
An |
groups |
A numeric |
groupnames |
A character |
addtext |
A character |
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 |
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
|
pch |
A numeric |
col |
A numeric or character |
pcs |
A character |
legend |
Boolean. Should a legend be added to the plot? Defaults to
|
main |
A character |
plot3d |
Boolean. If |
outside |
Boolean. If |
... |
Further arguments to be passed to |
This function returns nothing. It is called only for the side effect of producing a PCA plot or screeplot.
plotPCA,ExpressionSet-method
:
James W. MacDonald <jmacdon@u.washington.edu>
library("affy") data(sample.ExpressionSet) plotPCA(sample.ExpressionSet, groups = as.numeric(pData(sample.ExpressionSet)[,2]), groupnames = levels(pData(sample.ExpressionSet)[,2]))
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