plotPeak {TargetSearch} | R Documentation

## Plot peaks

### Description

Plot a peak of a given metabolite in a given sample showing the search windows.

### Usage

    plotPeak(samples, Lib, metProf, rawpeaks, which.smp=1, which.met=1,
    	massRange=NULL, corMass=FALSE)

### Arguments

`samples` | A `tsSample` object created by `ImportSamples` function.
`Lib` | A `tsLib` object created by `ImportLibrary` function.
`metProf` | A metabolite profile object. See `Profile`
`rawpeaks` | A three component list containing the retention time, the intensity matrix, and the mass range. See `peakCDFextraction`.
`which.smp` | A numeric value indicating the sample.
`which.met` | A numeric value indicating the metabolite.
`massRange` | A two component numeric vector with the scan mass range to extract. Use `NULL` for automatic detection.
`corMass` | Logical. If TRUE, show only correlating masses for the selected metabolite. Show all masses otherwise.

### Value

A two component list containing the retention time and the intensity matrices. This list can be recycled as the 'rawpeaks' parameter for further plots (for example in a loop), so the CDF file doesn't need to be read again.

### Note

This function was completely rewritten. For the old function, see `plotPeakSimple`.

In case the RI files are in text format and their column names are not standard (for example, when the files were generated with another software), use the global option `'TS_RI_columns'` or transform the RI files to `TargetSearch` binary format. See the documentation in function `text2bin`.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`plotPeakSimple`, `RIcorrect`, `tsMSdata`, `tsRim`, `peakCDFextraction`, `matplot`

### Examples

    require(TargetSearchData)
    data(TSExample)

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

    # Plot the peak "Valine" for sample number 1
    grep("Valine", libName(refLibrary)) # answer: 3

    # plot peak from the cdf file. The rawpeaks object can be recycled in order to plot
    # other metabolites.
    rawpeaks <- plotPeak(sampleDescription, refLibrary, metabProfile, which.smp=1,
            which.met=3, massRange=c(85,500), corMass=FALSE)

[Package TargetSearch version 1.48.0 Index]