xcms (version 1.48.0)

plot.xcmsEIC: 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, ...)

See Also

xcmsEIC-class, png, pdf, postscript,