plot.xcmsEIC: Plot extracted ion chromatograms from multiple files

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

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, [e-mail]

See Also

xcmsEIC-class, png, pdf, postscript,

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.