Plot EICs

August 19, 2011, 09:14:12 AM

Multiple file EIC's
The following code allow EICs to be plotted without the need for the diffreport. You can also subset the matrix (gt) to plot only certain features.

Code: [Select]

library(xcms)
library(faahKO)
xs<- group(faahko)
xs<- fillPeaks(xs)
gt<-groups(xs)
eics <- getEIC(xs, mzrange=gt, rtrange = 200, groupidx = 1:nrow(gt))
                                                                           
pdf(file.path("tmp/%003d.pdf"), onefile = FALSE)
## you can also use png(file.path("tmp/%003d.png"), h=768, w=1024)
plot(eics, xs)
dev.off()

Single file EICs
If you have a certain file you want to plot EIC's from then it's probably best to load the file into the xcmsRaw object type.
The following code will plot a single EIC for a single file:

Code: [Select]

library(faahKO)
cdfpath <- system.file("cdf", package = "faahKO")
cdffiles <- list.files(cdfpath, recursive = TRUE,full=T)
xr <- xcmsRaw(cdffiles[1])
xr
plotEIC(xr, m=c(550,551), rt=c(3200, 3800))

You might also want to look at the rawEIC plot type:

Code: [Select]

par(mfrow=c(2,1))
plotEIC(xr, m=c(550,551), rt=c(3200, 3800))
raweic<-rawEIC(xr, m=c(550,551), rt=c(3200,3800))
plot(xr@scantime[raweic$scan], raweic$intensity, type="l", main="EIC", xlab="RT (secs)", ylab="Intensity")