plotEIC-methods {xcms}R Documentation

Plot a list of EICs for each sample

Description

Batch plot a list of extracted ion chromatograms to the current graphics device or to files.

Arguments

object the xcmsSet object
eics list of EIC matricies as produced by link{getEIC}
peakrange matrix with named columns: mzmin, mzmax, rtmin, and rtmax
nums integer vector of indecies of EICs to plot
classlabel factor with class labels for each EIC matrix in the list
peakindex integer vector with indecies to the rows of the xcmsSet group matrix corresponding to the rows of the peakrange matrix
filebase base file name under which to save the numbered EICs, no image files are saved if missing
wh integer vector of length two with pixel width and height of the output PNG images
sleep seconds to pause between plotting EICs, only useful if filebase is missing and the plots are interactively output

Methods

object = "xcmsSet"
plotEIC(object, eics, peakrange, nums = seq(length = nrow(peakrange)), classlabel = sampclass(object), peakindex = NULL, filebase = character(), wh = c(640,480), sleep = 0)

See Also

xcmsSet-class


[Package xcms version 1.0.0 Index]