plotPeakSimple {TargetSearch} | R Documentation

## Plot peaks - simple (old) interface

### Description

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.

### 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`.

### Note

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.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`plotPeak`, `RIcorrect`, `tsMSdata`, `tsRim`, `peakCDFextraction`, `matplot`

### Examples

    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))

[Package TargetSearch version 1.48.0 Index]