highlightChromPeaks {xcms} | R Documentation

## Add definition of chromatographic peaks to an extracted chromatogram plot

### Description

The `highlightChromPeaks` function adds chromatographic peak definitions to an existing plot, such as one created by the `plot` method on a `Chromatogram` or `Chromatograms` object.

### Usage

    highlightChromPeaks(x, rt, mz, peakIds = character(),
      border = rep("00000040", length(fileNames(x))), lwd = 1, col = NA,
      type = c("rect", "point", "polygon"), whichPeaks = c("any", "within",
      "apex_within"), ...)

### Arguments

`x` | For `highlightChromPeaks`: `XCMSnExp` object with the detected peaks.
`rt` | For `highlightChromPeaks`: `numeric(2)` with the retention time range from which peaks should be extracted and plotted.
`mz` | `numeric(2)` with the mz range from which the peaks should be extracted and plotted.
`peakIds` | `character` defining the IDs (i.e. rownames of the peak in the `chromPeaks` table) of the chromatographic peaks to be highlighted in a plot.
`border` | colors to be used to color the border of the rectangles/peaks. Has to be equal to the number of samples in `x`.
`lwd` | `numeric(1)` defining the width of the line/border.
`col` | For `highlightChromPeaks`: color to be used to fill the rectangle (if `type = "rect"`) or the peak (for `type = "polygon"`).
`type` | the plotting type. See `plot` in base grapics for more details. For `highlightChromPeaks`: `character(1)` defining how the peak should be highlighted: `type = "rect"` draws a rectangle representing the peak definition, `type = "point"` indicates a chromatographic peak with a single point at the position of the peak's `"rt"` and `"maxo"` and `type = "polygon"` will highlight the peak shape. For `type = "polygon"` the color of the border and area can be defined with parameters `"border"` and `"col"`, respectively.
`whichPeaks` | `character(1)` specifying how peaks are called to be located within the region defined by `mz` and `rt`. Can be one of `"any"`, `"within"`, and `"apex_within"` for all peaks that are even partially overlapping the region, peaks that are completely within the region, and peaks for which the apex is within the region. This parameter is passed to the `type` argument of the `chromPeaks` function. See related documentation for more information and examples.
`...` | additional parameters to the `matplot` or `plot` function.

### Author(s)

Johannes Rainer

### Examples

    ## Read some files from the faahKO package.
    library(xcms)
    library(faahKO)
    faahko_3_files <- c(system.file('cdf/KO/ko16.CDF', package = "faahKO"),
                        system.file('cdf/KO/ko18.CDF', package = "faahKO"))

    od <- readMSData(faahko_3_files, mode = "onDisk")

    ## Peak detection using the 'matchedFilter' method. Note that we are using a
    ## larger binSize to reduce the runtime of the example.
    xod <- findChromPeaks(od, param = MatchedFilterParam(binSize = 0.3, snthresh = 20))

    ## Extract the ion chromatogram for one chromatographic peak in the data.
    chrs <- chromatogram(xod, rt = c(2700, 2900), mz = 335)

    plot(chrs)

    ## Extract chromatographic peaks for the mz/rt range (if any).
    chromPeaks(xod, rt = c(2700, 2900), mz = 335)

    ## Highlight the chromatographic peaks in the area
    ## Show the peak definition with a rectangle
    highlightChromPeaks(xod, rt = c(2700, 2900), mz = 335)

    ## Color the actual peak
    highlightChromPeaks(xod, rt = c(2700, 2900), mz = 335,
        col = c("#ff000020", "#00ff0020"), type = "polygon")

[Package xcms version 3.6.2 Index]