plotPeakSimple: Plot peaks - simple (old) interface
In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

Description Usage Arguments Note Author(s) See Also Examples

Plot selected ions in a given time range. This is the old plot peak interface. Note: This function is considered deprecated and its usage is discouraged.

1 2	plotPeakSimple(rawpeaks, time.range, masses, cdfFile = NULL, useRI = FALSE, rimTime = NULL, standard = NULL, massRange = NULL, ...)

`rawpeaks`	A three component list containing the retention time, the intensity matrix, and the mass range. See `peakCDFextraction`.
`time.range`	The time range to plot in retention time or retention time index units to plot.
`masses`	A vector containing the ions or masses to plot.
`cdfFile`	The name of a CDF file. If a file name is specified, the ions will be extracted from there instead of using `rawpeaks`.
`useRI`	Logical. Whether to use Retention Time Indices or not.
`rimTime`	A retention time matrix of the found retention time markers. It is only used when `useRI` is `TRUE`.
`standard`	A numeric vector with RI values of retention time markers. It is only used when `useRI` is `TRUE`.
`massRange`	A two component numeric vector with the scan mass range to extract or `NULL` for automatic detection.
`...`	Further options passed to `matplot`.

This function used to be named 'plotPeak'. This function was completely rewritten so we kept the old version and renamed it 'plotPeakSimple'.

Important: This function is considered deprecated, though it is not yet labeled as such. This function can still be used to plot peaks for CDF files version 3 without the need to convert them to CDF format 4.

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

plotPeak, RIcorrect, tsMSdata, tsRim, peakCDFextraction, matplot

require(TargetSearchData)
data(TSExample)

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

# Plot the peak "Valine" for sample number 1
grep("Valine", libName(refLibrary)) # answer: 3
# select the first file
cdfFile  <- CDFfiles(sampleDescription)[1]

# select "Valine" top masses
top.masses <- topMass(refLibrary)[[3]]

# plot peak from the cdf file
plotPeakSimple(cdfFile = cdfFile, time.range = libRI(refLibrary)[3] + c(-2000,2000),
    masses = top.masses, useRI = TRUE, rimTime = RImatrix[,1],
    standard = rimStandard(rimLimits), massRange = c(85, 500))

# the same, but extracting the peaks into a list first. This may be better if
# you intend to loop through several peaks.
rawpeaks <- peakCDFextraction(cdfFile, massRange = c(85,500))
plotPeakSimple(rawpeaks, time.range = libRI(refLibrary)[3] + c(-2000,2000),
    masses = top.masses, useRI = TRUE, rimTime = RImatrix[,1],
    standard = rimStandard(rimLimits), massRange = c(85, 500))