
Many thanks Kevin,

As a result of your advice, and that of other helpful experts, I ended up with the following script, which worked brilliantly:


cat <-read.table("R855868825matrix.csv", sep=",", header=T)

 head (cat, n=24)

catopsis = cat[,-1]
row.names(catopsis) = cat$sample

pca <- prcomp (t(catopsis))

plot(pca, catopsis [])

summary(prcomp(catopsis))

biplot(prcomp(catopsis, scale = TRUE))

  ----- Original Message ----- 
  From: Kevin Wright-5 [via R] 
  To: colin1 
  Sent: Monday, January 25, 2010 5:04 PM
  Subject: Re: [R] PCA: Showing file datalabels on biplot


  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 <[hidden email]>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. 
  > 
  > ______________________________________________ 
  > [hidden email] 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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  and provide commented, minimal, self-contained, reproducible code. 



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