plotSpectra: Plot a Spectra Comparison

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

Description

plotSpectra plots a contrast between the reference spectra and the median spectra of a given metabolite in the library. plotAllRIdev saves the plots of the median-reference spectra comparisons of all the metabolites in the reference library into a PDF file.

Usage

plotSpectra(Lib, peaks, libId = 1, type = "ht")

plotAllSpectra(Lib, peaks, type = "ht", 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.
type	The type of the plot. Options are "ht", head-tail plot, "ss", side by side plot, and "diff", spectrum difference 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.

Details

The median spectra is obtained by computing the median intensity of every ion across the samples. The median and the reference spectra values are scaled to vary between 0 and 999 in order to make them comparable.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

tsLib, tsMSdata,pdf

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 a comparison RI deviation of metabolite "Valine"
grep("Valine", libName(refLibrary)) # answer: 3
plotSpectra(refLibrary, peakData, libId = 3, type = "ht")

# Plot the spectra "side by side"
plotSpectra(refLibrary, peakData, libId = 3, type = "ss")

# Plot the spectra difference
plotSpectra(refLibrary, peakData, libId = 3, type = "diff")

TargetSearch documentation built on March 12, 2021, 2 a.m.