R help - Jan 2010 - PCA: Showing file datalabels on biplot

The script below successfully produces a biplot of the data but the 'site
names' (rows) and the names of the 'response variables' (columns)
are shown
as simple numerals (rather than the column and row names). How might I
'enforce' the use of the row/column names used in the datafile (section
of
datafile shown below)?
Can anyone help, please?

Section of datafile

sample	a	b	c	d ---n42
HBR-6	1	1	1	1
HBR-7	1	1	1	2
HBR-8	1	1	1	1
HBR-9	1	1	1	2
HBR-10	1	1	1	1
HBR-11	1	1	1	1
HBR-12	1	1	1	1
HBR-13	1	1	1	1
HBR-14	2	1	2	2
HBR-15	2	1	2	1
HBR-16	1	1	2	1
HBR-17	1	1	2	1
HBR-18	1	1	2	1
HBR-19	1	1	2	1
HBR-20	1	1	2	1
HBR-21	1	2	1	1
HBR-30	1	1	2	2
HBR-31	1	2	1	2
HBR-32	2	2	1	2
HBR-33	1	2	1	2
HBR-34	1	2	2	2
HBR-35	1	2	2	1
HBR-36	1	2	1	2
HBR-37	1	2	1	2


cat <-read.table("R855868825matrix.csv", sep=",",
header=T)
 head (cat, n=24)
catopsis <- (cbind(cat$a, cat$b, cat$c, cat$d, cat$e, cat$f, cat$g, cat$h,
cat$i, cat$j, cat$k, cat$l, cat$m, cat$n, cat$o, cat$p, cat$q, cat$r, cat$s,
cat$t, cat$u, cat$v, cat$w, cat$x, cat$y, cat$z, cat$aa, cat$ab, cat$ac,
cat$ad, cat$ae, cat$af, cat$ag, cat$ah, cat$ai, cat$aj, cat$ak, cat$al,
cat$am, cat$an, cat$ao, cat$ap))
pca <- prcomp (t(catopsis))
plot(pca, catopsis [])
summary(prcomp(catopsis))
biplot(prcomp(catopsis, scale = TRUE))

-- 
View this message in context:
http://n4.nabble.com/PCA-Showing-file-datalabels-on-biplot-tp1289524p1289524.html
Sent from the R help mailing list archive at Nabble.com.

str(catopsis) shows no labels, so how can biplot know what to use?

Try this before call prcomp:

colnames(catopsis) <- c('a','b','c','d')
rownames(catopsis) <- cat$sample

Also, see the 'reshape' package for easier data manipulation.

Kevin


On Mon, Jan 25, 2010 at 10:39 AM, colin1
<colinhindmarch@talktalk.net>wrote:
>
> The script below successfully produces a biplot of the data but the
'site
> names' (rows) and the names of the 'response variables'
(columns) are shown
> as simple numerals (rather than the column and row names). How might I
> 'enforce' the use of the row/column names used in the datafile
(section of
> datafile shown below)?
> Can anyone help, please?
>
> Section of datafile
>
> sample  a       b       c       d ---n42
> HBR-6   1       1       1       1
> HBR-7   1       1       1       2
> HBR-8   1       1       1       1
> HBR-9   1       1       1       2
> HBR-10  1       1       1       1
> HBR-11  1       1       1       1
> HBR-12  1       1       1       1
> HBR-13  1       1       1       1
> HBR-14  2       1       2       2
> HBR-15  2       1       2       1
> HBR-16  1       1       2       1
> HBR-17  1       1       2       1
> HBR-18  1       1       2       1
> HBR-19  1       1       2       1
> HBR-20  1       1       2       1
> HBR-21  1       2       1       1
> HBR-30  1       1       2       2
> HBR-31  1       2       1       2
> HBR-32  2       2       1       2
> HBR-33  1       2       1       2
> HBR-34  1       2       2       2
> HBR-35  1       2       2       1
> HBR-36  1       2       1       2
> HBR-37  1       2       1       2
>
>
> cat <-read.table("R855868825matrix.csv", sep=",",
header=T)
>  head (cat, n=24)
> catopsis <- (cbind(cat$a, cat$b, cat$c, cat$d, cat$e, cat$f, cat$g,
cat$h,
> cat$i, cat$j, cat$k, cat$l, cat$m, cat$n, cat$o, cat$p, cat$q, cat$r,
> cat$s,
> cat$t, cat$u, cat$v, cat$w, cat$x, cat$y, cat$z, cat$aa, cat$ab, cat$ac,
> cat$ad, cat$ae, cat$af, cat$ag, cat$ah, cat$ai, cat$aj, cat$ak, cat$al,
> cat$am, cat$an, cat$ao, cat$ap))
> pca <- prcomp (t(catopsis))
> plot(pca, catopsis [])
> summary(prcomp(catopsis))
> biplot(prcomp(catopsis, scale = TRUE))
>
> --
> View this message in context:
>
http://n4.nabble.com/PCA-Showing-file-datalabels-on-biplot-tp1289524p1289524.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> 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

	[[alternative HTML version deleted]]