It exists a method for plotting EICs from a xcmsSet.
You can use this methods for your problem, because the original xcmsSet object is stored within a xsAnnotate object.
So with xs <- object@xcmsSet (object is here the processed xsAnnotate object)
you can retrieve the original xcmsSet object.
Here with an example
library(xcms)
library(faahKO)
cdfpath <- system.file("cdf", package = "faahKO")
cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
xset <- xcmsSet(cdffiles)
xset <- group(xset)
xsa <- annotate(xset)
##Only for the case the xset is lost.
xset <- xsa@xcmsSet
##For plotting first fillPeaks your xcmsSet
xset.fill <- fillPeaks(xset)
##Get EICs
xeic <- getEIC(xset.fill, groupidx=1:nrow(xsa@groupInfo))
##Plot EICs for the first peak
plot(xeic, groupidx=1)
## For more information about this function see ?xcms::plot.xcmsEIC
Cheers,
Carsten