plot.xcmsEIC {xcms} | R Documentation

## Plot extracted ion chromatograms from multiple files

### Description

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

### Arguments

`x` | the `xcmsEIC` object
`y` | optional `xcmsSet` object with peak integration data
`groupidx` | either character vector with names or integer vector with indicies of peak groups for which to plot EICs
`sampleidx` | either character vector with names or integer vector with indicies of samples for which to plot EICs
`rtrange` | a two column matrix with minimum and maximum retention times between which to return EIC data points if it has the same number of rows as the number groups in the `xcmsEIC` object, then `sampleidx` is used to subset it. otherwise, it is repeated over the length of `sampleidx` it may also be a single number specifying the time window around the peak for which to plot EIC data
`col` | color to use for plotting extracted ion chromatograms. if missing and `y` is specified, colors are taken from `unclass(sampclass(y))` and the default palette if it is the same length as the number groups in the `xcmsEIC` object, then `sampleidx` is used to subset it. otherwise, it is repeated over the length of `sampleidx`
`legtext` | text to use for legend. if `NULL` and `y` is specified, legend text is taken from the sample class information found in the `xcmsSet`
`peakint` | logical, plot integrated peak area with darkened lines (requires that `y` also be specified)
`sleep` | seconds to pause between plotting EICs
`...` | other graphical parameters

### Value

A `xcmsSet` object.

### Methods

x = "xcmsEIC"

  `plot.xcmsEIC(x, y, groupidx = groupnames(x), sampleidx = sampnames(x), rtrange = x@rtrange, col = rep(1, length(sampleidx)), legtext = NULL, peakint = TRUE, sleep = 0, ...)`

### Author(s)

Colin A. Smith, csmith@scripps.edu

### See Also

`xcmsEIC-class`, `png`, `pdf`, `postscript`,

[Package xcms version 3.6.2 Index]