plotPeakRI {TargetSearch} | R Documentation

## Plot peak RI across samples

### Description

Plot peak RI of the quant mass of a given metabolite across samples. This function can be used to visualize the elution time of a metabolite in the RI and RT dimension, and in combination with the function `sampleRI` for fine tunning.

### Usage

    plotPeakRI(samples, Lib, libID, dev=NULL, mz=NULL, RI=NULL,
               method=c('RI', 'Intensity'), useRI=TRUE, main=NULL,
               col=NULL, int_range=c(2,6), cex_range=c(.7,6), key_width=2)

### Arguments

`samples` | A `tsSample` object created by `ImportSamples` function.
`Lib` | A `tsLib` object created by `ImportLibrary` function.
`libID` | An index (integer or character) value representing the respective metabolite in the reference library `Lib`.
`dev` | The allowed retention index (RI) deviation or `NULL`.
`mz` | A list of m/z values to search or `NULL`.
`RI` | The expected retention index or `NULL`.
`method` | A character vector used to decided what peak should be chosen in case there are ambiguous peaks. If `'RI'`, then the closest peak to the expected RI is chosen. If `'Intensity'`, then the highest is taken.
`useRI` | Logical. Should the RI or RT be displayed in the y-axis?
`main` | The title for the plot. If `NULL`, then the metabolite name is displayed.
`col` | A color vector (length > 2) to show different levels of peak intensity.
`int_range` | A length-two vector. The limits of the intensity for the color key. Note the the intensity is expressed in log10. Eg, a value of 2 represents a intensity of 100.
`cex_range` | The 'cex' range value of the points. lower-intense peaks are represented as points of smaller size.
`key_width` | The width in cm of the area allocated for the color key.

### Details

This function uses internally `FindAllPeaks`, so the same rules apply, i.e., the parameters `dev`, `mz`, and `RI` have preference over the settings of the metabolite indexed by `libID`.

In the plot, the x-axis are samples as defined by the object `samples`. The y-axis is retention index (RI) as shown on the left-hand-size. On the right-hand-size y-axis the approximate retention time (RT) is shown. This is because the RT varies across samples, therefore it is averaged for displays purposes. If `useRI==FALSE`, then the RT is displayed on the left hand size and the RI is averaged and shown on the left. Note that in either case, the RI is used for searching.

The point size is proportional to the log10 of the peak intensity. Their size is controlled by the parameters `int_range` and `cex_range`. By default, intensities of 100 (log10 => 2) or lower are shown with `cex=0.7`, while intensities greater than 1000000 (log10 => 6) as displaued with `cex=6`. This also affects the scaling of the color key.

The best peaks, selected acording to `method`, are shown with a black border, while the other are shown with no border and slightly transparent.

The output is the RI of the best peaks or invisible. Note that if no peak is found, then no plot is drawn.

### Value

Returns invisible or a numeric vector with the corresponding RI of the best peak chosen by `method`.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`FindAllPeaks`, `sampleRI`, `ImportSamples`, `ImportLibrary`

### Examples

    def.par <- par(no.readonly = TRUE) # save parameters for resetting

    # load pre-calculated example data files and objects
    require(TargetSearchData)
    data(TSExample)

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

    # search all peaks of Valine (GC.3) and selective masses. Retention index
    ri <- plotPeakRI(sampleDescription, refLibrary, 'GC.3')

    # increase deviation, change m/z to search, change colors and title
    main <- 'Valine'
    cols <- c('red', 'blue', 'green')
    ri <- plotPeakRI(sampleDescription, refLibrary, 'GC.3', dev=4000, mz=144,
                     main=main, col=cols)

    # plot by RT instead. Note the RI is still returned
    ri <- plotPeakRI(sampleDescription, refLibrary, 'GC.3', useRI=FALSE)

    par(def.par) # reset to default

[Package TargetSearch version 1.48.0 Index]