plotPeakSimple {TargetSearch} | R Documentation |
Plot selected ions in a given time range.
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 |
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 |
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 |
standard |
A numeric vector with RI values of retention time markers. It is only used
when |
massRange |
A two component numeric vector with the scan mass range to extract or
|
... |
Further options passed to |
This function used to be named 'plotPeak'. This function was completely rewritten so we kept the old version and renamed it 'plotPeakSimple'.
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))