Sam,
There are many different packages to show your data as heatmaps. I've outlined some code below which should hopefully be useful.
library(xcms)
library(faahKO)
cdfpath <- system.file("cdf", package = "faahKO")
cdffiles <- list.files(cdfpath, recursive = TRUE,full=T)
faahko <- xcmsSet(cdffiles)
faahko <- group(faahko)
The above loads the faahko toy dataset. You can skip this step and use your own data. I'm just using it for demo purposes.
values<-groupval(faahko) ## gets the raw values of each feature from each file
image(values) ## a simple heatmap
library(lattice)
levelplot(values) ## a nicer heatmap look at the the help for more details ie ?levelplot
library(gplots) ## a very good graphics library
heatmap.2(values, Rowv=F, Colv=F, dendrogram="none", trace="none", scale="none", col=redgreen)
## probably more what you want. You can scale the data to z values using scale="row"
## might also want to look at the dendrogram cluster
heatmap.2(values, Rowv=F, Colv=T, dendrogram="col", trace="none", scale="row", col=redgreen)
I would also suggest looking at this site for general R help:
http://www.statmethods.net/
and for the heapmaps:
http://www2.warwick.ac.uk/fac/sci/moac/ ... r/heatmap/