R: Plot Retention Time Index Deviation

plotRIdev {TargetSearch}

R Documentation

Plot Retention Time Index Deviation

Description

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.

Usage

plotRIdev(Lib, peaks, libId = 1)

plotAllRIdev(Lib, peaks, pdfFile, width = 8, height = 8, ...)

Arguments

`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`.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

Examples

require(TargetSearchData)
data(TSExample)

# 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")