plotRIdev {TargetSearch} | R Documentation

## Plot Retention Time Index Deviation

### Description

`plotRIdev` plots the Retention Time Index Deviation of a given set of metabolites. `plotAllRIdev` saves the plots of the RI deviations of all the metabolites in the library object into a PDF file.

### Usage

    plotRIdev(Lib, peaks, libId = 1)

    plotAllRIdev(Lib, peaks, pdfFile, width = 8, height = 8, ...)

### Arguments

`Lib` | A `tsLib` object created by `ImportLibrary` function.
`peaks` | A `tsMSdata` object. See `peakFind`.
`libId` | A numeric vector providing the indices of the metabolites to plot.
`pdfFile` | A file name where the plot will be saved. Only `plotAllRIdev`.
`width, height` | The width and height of the plots in inches. Only `plotAllRIdev`.
`...` | Further options passed to `pdf`.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`ImportLibrary`, `tsLib`, `tsMSdata`, `pdf`

### Examples

    require(TargetSearchData)
    data(TSExample)

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

    peakData <- peakFind(sampleDescription, refLibrary, corRI)

    # Plot RI deviation of metabolite "Valine"
    grep("Valine", libName(refLibrary)) # answer: 3
    plotRIdev(refLibrary, peakData, libId = 3)

    # Plot an RI deviation overview of the first nine metabolites
    plotRIdev(refLibrary, peakData, libId = 1:9)

    # Save all RI deviation into a pdf file
    plotAllRIdev(refLibrary, peakData, pdfFile = "RIdeviations.pdf")

[Package TargetSearch version 1.43.3 Index]