ggplot2 Version of highlightChromPeaks()

Adds chromatographic peak annotations to existing chromatogram plots. This is a ggplot2 implementation that works with XCMSnExp or XcmsExperiment objects, highlighting detected peaks with rectangles, points, or polygons.

Usage

ghighlightChromPeaks(
  object,
  rt = numeric(),
  mz = numeric(),
  peakIds = character(),
  border = "#00000040",
  fill = NA,
  type = c("rect", "point", "polygon"),
  whichPeaks = c("any", "within", "apex_within")
)

# S4 method for class 'XCMSnExp'
ghighlightChromPeaks(
  object,
  rt = numeric(),
  mz = numeric(),
  peakIds = character(),
  border = "#00000040",
  fill = NA,
  type = c("rect", "point", "polygon"),
  whichPeaks = c("any", "within", "apex_within")
)

# S4 method for class 'XcmsExperiment'
ghighlightChromPeaks(
  object,
  rt = numeric(),
  mz = numeric(),
  peakIds = character(),
  border = "#00000040",
  fill = NA,
  type = c("rect", "point", "polygon"),
  whichPeaks = c("any", "within", "apex_within")
)

Arguments

object

An XCMSnExp or XcmsExperiment object with detected peaks.

rt

numeric(2) vector of length 2 specifying retention time range for peak extraction (optional).

mz

numeric(2) vector of length 2 specifying m/z range for peak extraction (optional).

peakIds

character vector of peak identifiers (rownames from xcms::chromPeaks() to highlight. If provided, rt and mz are ignored.

border

Color for peak borders (default: semi-transparent grey).

fill

Color for peak fills (default: NA).

type

character(1) specifying visualization type: "rect" (rectangle), "point" (apex point), or "polygon" (peak shape). Default: "rect".

whichPeaks

character(1) specifying peak selection: "any" (any overlap), "within" (fully contained), or "apex_within" (apex in range). Default: "any".

Value

A list of ggplot2 layer objects that can be added to an existing ggplot chromatogram.

Details

This function returns ggplot2 layers (geoms) that can be added to an existing chromatogram plot using the + operator. Unlike the base R version which modifies an existing plot, this returns composable layers.

Like the original xcms::highlightChromPeaks(), this function takes the full XCMSnExp/XcmsExperiment object and searches all peaks across all samples, then filters by rt/mz. This means it can highlight peaks from multiple samples. To highlight only peaks from a specific sample, filter the object first using filterFile().

See also

xcms::highlightChromPeaks() for the original xcms implementation

Author

Jan Stanstrup

Examples

library(xcmsVis)
library(xcms)
#> Loading required package: BiocParallel
#> 
#> This is xcms version 4.8.0 
library(faahKO)
library(MsExperiment)
#> Loading required package: ProtGenerics
#> 
#> Attaching package: ‘ProtGenerics’
#> The following object is masked from ‘package:stats’:
#> 
#>     smooth
library(ggplot2)

# Load and process example data
cdf_files <- system.file("cdf/KO/ko15.CDF", package = "faahKO")
xdata <- readMsExperiment(spectraFiles = cdf_files,
                          BPPARAM = BiocParallel::SerialParam())
xdata <- findChromPeaks(xdata, param = xcms::CentWaveParam(),
                        BPPARAM = BiocParallel::SerialParam())

# Extract chromatogram for plotting
chr <- chromatogram(xdata, mz = c(200, 210), rt = c(2500, 3500))
#> Extracting chromatographic data
#> Processing chromatographic peaks

# Highlight peaks from the full dataset (all samples in xdata)
gplot(chr[1, 1], peakType = "none") +
  ghighlightChromPeaks(xdata, rt = c(2500, 3500), mz = c(200, 210))


# Or filter to single sample first for cleaner visualization
xdata_filtered <- filterFile(xdata, 1)
gplot(chr[1, 1], peakType = "none") +
  ghighlightChromPeaks(xdata_filtered, rt = c(2500, 3500), mz = c(200, 210))