plotPeak {TargetSearch} | R Documentation |
Plot a peak of a given metabolite in a given sample showing the search windows.
plotPeak(samples, Lib, metProf, rawpeaks, which.smp=1, which.met=1, massRange=NULL, corMass=FALSE)
samples |
A |
Lib |
A |
metProf |
A metabolite profile object. See |
rawpeaks |
A thre component list containing the retention time, the intensity matrix,
and the mass range. See |
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. or
|
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
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)