I think this should help:
require(pcaMethods)
data(metaboliteDataComplete)
mdc <- scale(metaboliteDataComplete, center=TRUE, scale=FALSE)
## Now create 5% of outliers.
cond <- runif(length(mdc)) < 0.05;
mdcOut <- mdc
mdcOut[cond] <- 10
## Now we do a conventional PCA and robustPca on the original
and the data
## with outliers.
## We use center=FALSE here because the large artificial outliers
would
## affect the means and not allow to objectively compare the
results.
resSvd <- pca(mdc, method = "svd", nPcs = 10, center =
FALSE)
resSvdOut <- pca(mdcOut, method = "svd", nPcs = 10, center =
FALSE)
resRobPca <- pca(mdcOut, method = "robustPca", nPcs = 10, center
= FALSE)
biplot(resRobPca) # Draw the graph
biplot # shows the generic
methods("biplot") # which method is used? Depends on the class of the
object
class(resRobPca) # the class is 'pcaRes'
biplot.pcaRes # show the actual code for drawing the object
Kevin
On Tue, Apr 24, 2012 at 1:44 PM, Michael <comtech....@gmail.com> wrote:
> > biplot
>
> standardGeneric for "biplot" defined from package "stats"
>
> function (x, ...)
>
> standardGeneric("biplot")
>
> <environment: 0x0d4444d8>
>
> Methods may be defined for arguments: x
>
> Use showMethods("biplot") for currently available ones.
>
> >
>
> >
>
> > showMethods("biplot")
>
> Function: biplot (package stats)
>
> x="ANY"
>
> x="character"
>
> (inherited from: x="ANY")
>
> x="Pca"
>
> > biplot(resRobPCA)
>
> But how do I get the source code of "biplot"?
>
> Thank you!
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Kevin Wright
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