R help - Jun 2008 - plotting prcomp

Please consider the following PCA example;

my.df <-
  data.frame(A=(x <- rnorm(100,mean=100, sd=10)),
             B=(y <- x + rnorm(100,mean=10, sd=10)))

plot(my.df)

my.pc <-
  prcomp(my.df, center=TRUE, scale=TRUE)

biplot(my.pc)

my.x <- (my.pc$x)[,1]
my.y <- (my.pc$x)[,2]

plot(my.x, my.y, type="n")
text(my.x, my.y, labels=1:100)

Clearly the plots have the same relative values, but I can't work out how
the second plot is relative to the first. I have been reading the manual,
but I still can't work it out.

Can anyone show me the code to generate the data that I see plotted using
biplot? What am I missing?

Dan.

	[[alternative HTML version deleted]]

On Fri, 27 Jun 2008, Dan Bolser wrote:
> Please consider the following PCA example;
>
> my.df <-
>  data.frame(A=(x <- rnorm(100,mean=100, sd=10)),
>             B=(y <- x + rnorm(100,mean=10, sd=10)))
>
> plot(my.df)
>
> my.pc <-
>  prcomp(my.df, center=TRUE, scale=TRUE)
>
> biplot(my.pc)
>
> my.x <- (my.pc$x)[,1]
> my.y <- (my.pc$x)[,2]
>
> plot(my.x, my.y, type="n")
> text(my.x, my.y, labels=1:100)
>
> Clearly the plots have the same relative values, but I can't work out
how
> the second plot is relative to the first. I have been reading the manual,
> but I still can't work it out.
>
> Can anyone show me the code to generate the data that I see plotted using
> biplot? What am I missing?
Reading the references on ?biplot.prcomp, or a good book on the subject 
(such as MASS or Gower & Hand).

A biplot is a specific type of plot and the help page does not spell out 
the rather mathematical details (and there are several variants).
>
> Dan.
>
> 	[[alternative HTML version deleted]]
>
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>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595