plotPeak: Plot peaks
In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

Description Usage Arguments Value Note Author(s) See Also Examples

Plot a peak of a given metabolite in a given sample showing the search windows.

1 2	plotPeak(samples, Lib, metProf, rawpeaks, which.smp=1, which.met=1, massRange=NULL, corMass=FALSE)

`samples`	A `tsSample` object created by `ImportSamples` function.
`Lib`	A `tsLib` object created by `ImportLibrary` function.
`metProf`	A metabolite profile object. See `Profile`
`rawpeaks`	A three component list containing the retention time, the intensity matrix, and the mass range. See `peakCDFextraction`.
`which.smp`	A numeric value indicating the sample.
`which.met`	A numeric value indicating the metabolite.
`massRange`	A two component numeric vector with the scan mass range to extract. Use `NULL` for automatic detection.
`corMass`	Logical. If TRUE, show only correlating masses for the selected metabolite. Show all masses otherwise.

A two component list containing the retention time and the intensity matrices. This list can be recycled as the 'rawpeaks' parameter for further plots (for example in a loop), so the CDF file doesn't need to be read again.

This function was completely rewritten. For the old function, see plotPeakSimple.

In case the RI files are in text format and their column names are not standard (for example, when the files were generated with another software), use the global option 'TS_RI_columns' or transform the RI files to TargetSearch binary format. See the documentation in function text2bin.

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

plotPeakSimple, RIcorrect, tsMSdata, tsRim, peakCDFextraction, matplot

require(TargetSearchData)
data(TSExample)

# update CDF and RI paths
CDFpath(sampleDescription) <- file.path(find.package("TargetSearchData"), "gc-ms-data")
RIpath(sampleDescription) <- file.path(find.package("TargetSearchData"), "gc-ms-data")

# Plot the peak "Valine" for sample number 1
grep("Valine", libName(refLibrary)) # answer: 3

# plot peak from the cdf file. The rawpeaks object can be recycled in order to plot
# other metabolites.
rawpeaks <- plotPeak(sampleDescription, refLibrary, metabProfile, which.smp=1,
        which.met=3, massRange=c(85,500), corMass=FALSE)