plot.xcmsEIC {xcms} | R Documentation |
Batch plot a list of extracted ion chromatograms to the current graphics device.
plot.xcmsEIC(x, y, groupidx = groupnames(x), sampleidx = sampnames(x), rtrange = x@rtrange, col = rep(1, length(sampleidx)), legtext = NULL, peakint = TRUE, sleep = 0, ...)
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 |
A xcmsSet
object.
Colin A. Smith, csmith@scripps.edu
xcmsEIC-class
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