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, border = rep("00000040", length(fileNames(x))),
  lwd = 1, col = NA, type = c("rect", "point"), ...)

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.

border

colors to be used to color the border of the rectangles. 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.

type

the plotting type. See plot 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".

...

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
highlightChromPeaks(xod, rt = c(2700, 2900), mz = 335)
[Package xcms version 3.0.2 Index]