R help - Apr 2012 - How do i read the source code of "biplot"?

> 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!

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You have another package using an S4 for biplot -- vanilla R doesn't
seem to set that generic...

Anyways, the function you need is getMethod()

Michael

On Tue, Apr 24, 2012 at 2:44 PM, Michael <comtech.usa at 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]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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.usa@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]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> 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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