| plotRIdev {TargetSearch} | R Documentation |
plotRIdev plots the Retention Time Index Deviation of a given set of metabolites.
plotAllRIdev saves the plots of the RI deviations of all the metabolites in the library object
into a PDF file.
plotRIdev(Lib, peaks, libId = 1) plotAllRIdev(Lib, peaks, pdfFile, width = 8, height = 8, ...)
Lib |
A tsLib object created by ImportLibrary function. |
peaks |
A tsMSdata object. See peakFind. |
libId |
A numeric vector providing the indices of the metabolites to plot. |
pdfFile |
A file name where the plot will be saved. Only plotAllRIdev. |
width, height |
The width and height of the plots in inches. Only plotAllRIdev. |
... |
Further options passed to pdf. |
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
ImportLibrary, tsLib,
tsMSdata, pdf
require(TargetSearchData)
data(TargetSearchData)
# get RI file path
RI.path <- file.path(.find.package("TargetSearchData"), "gc-ms-data")
# update RI file path
RIpath(sampleDescription) <- RI.path
peakData <- peakFind(sampleDescription, refLibrary, corRI)
# Plot RI deviation of metabolite "Valine"
grep("Valine", libName(refLibrary)) # answer: 3
plotRIdev(refLibrary, peakData, libId = 3)
# Plot an RI deviation overview of the first nine metabolites
plotRIdev(refLibrary, peakData, libId = 1:9)
# Save all RI deviation into a pdf file
plotAllRIdev(refLibrary, peakData, pdfFile = "RIdeviations.pdf")