plotPCA {facopy} | R Documentation |
Plot a PCA of the samples based on their similarity given a certain set of alterations.
plotPCA(fad, alteration, varName, sel = NULL, design = c("binary", "versus", "lvog")[1], do.plot = TRUE, by.size = TRUE, cex = 4)
fad |
|
alteration |
A character describing the kinds of alteration to include. It should be one of the following: |
varName |
A character indicating the variable of interest within the |
sel |
A character vector with the chromosome arms that will be taken into account in the analysis. Example: |
design |
Depending on the chosen alteration, different designs are available. The simplest design is |
do.plot |
A logical indicating whether to produce graphical output. |
by.size |
A logical indicating whether the width of the points' border represents the frequency of the selected alterations. |
cex |
A numerical value giving the amount by which points in the plot should be scaled relative to the base size. Default is 4. |
The results of the PCA are returned and the graphical output is optional.
David Mosen-Ansorena
data(myStudy) # load example study pca = plotPCA(myStudy, "any", "stage") head(pca$eig)