putting samples in order on plots

[Hparker]

Hi all,

I am importing in the files produced from the bismark methylation extractor tool (bedgraphs and cov files) and producing plots to look at the quality of the data. I have 48 samples and would like to order the samples in a particular order along the x-axis of the plots I have created. I first read in the files using read.bismark from a folder. To try and solve this I then created a csv file with the samples in the order I would like them to be in and imported this into R - but when I then used later code to apply names I got the following error (which did not happen with the files I imported using read.bismark):

Error in as.character.default(x) : 
  no method for coercing this S4 class to a vector

So I resorted back to read.bismark to import the files. So my question is how can I reorder the samples along the x-axis in R? Can I add this information to the code I already have for creating the plots? Eg. code for one of the plots:

pdf("meth_by_region.pdf",w=10,h=6);
par(mai=c(2,.8,.8,.4)); 
ur <- unique(bfu$Region)
for(i in 1:length(ur)) {
  k <- bfu$Region==ur[i]
  boxplot( as.data.frame(meth[k,]), las=2, main=ur[i]);
}
dev.off()

Thanks in advance for your help!