TargetSearch (version 1.28.1)

plotPeakSimple: Plot peaks - simple interface

Description

Plot selected ions in a given time range.

Usage

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

Arguments

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.

See Also

plotPeak, 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
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))