EIC color

September 16, 2013, 09:07:07 AM

Hi everyone,
One simple question : Is it possible to choose the color of the EICs generated with GetEIC ?
Because i have multiple classes of samples and i plot EICs for every class and one comes in yellow which is an eyes killer!

Many thanks for your help!

Re: EIC color

Reply #1 – September 18, 2013, 12:30:22 PM

Musca,

Yes have a look at :

help("plot.xcmsEIC")

Quote

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