plotPeak {TargetSearch}R Documentation

Plot peaks

Description

Plot selected ions in a given time range.

Usage

plotPeak(rawpeaks, time.range, masses, cdfFile = NULL,  useRI = FALSE,
         rimTime = NULL, standard = NULL, massRange = c(85, 500), ...)

Arguments

rawpeaks A two component list containing the retention time and the intensity matrices. 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.
... Further options passed to matplot.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

RIcorrect, tsMSdata, tsRim, peakCDFextraction, matplot

Examples

require(TargetSearchData)
data(TargetSearchData)

# 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
plotPeak(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))
plotPeak(rawpeaks, time.range = libRI(refLibrary)[3] + c(-2000,2000),
    masses = top.masses, useRI = TRUE, rimTime = RImatrix[,1],
    standard = rimStandard(rimLimits), massRange = c(85, 500))


[Package TargetSearch version 1.0.0 Index]