ggplot2 Version of plotChromPeaks()

Visualizes identified chromatographic peaks as rectangles in the retention time vs. m/z plane. This is a ggplot2 implementation of xcms's xcms::plotChromPeaks() function, enabling modern visualization and interactive plotting capabilities.

Usage

gplotChromPeaks(
  object,
  file = 1,
  xlim = NULL,
  ylim = NULL,
  border = "#00000060",
  fill = NA,
  msLevel = 1L
)

# S4 method for class 'XCMSnExp'
gplotChromPeaks(
  object,
  file = 1,
  xlim = NULL,
  ylim = NULL,
  border = "#00000060",
  fill = NA,
  msLevel = 1L
)

# S4 method for class 'XcmsExperiment'
gplotChromPeaks(
  object,
  file = 1,
  xlim = NULL,
  ylim = NULL,
  border = "#00000060",
  fill = NA,
  msLevel = 1L
)

Arguments

object

An XCMSnExp or XcmsExperiment object with detected chromatographic peaks.

file

integer(1) specifying which file/sample to plot (default: 1).

xlim

numeric(2) vector of length 2 specifying retention time range. If NULL (default), uses full retention time range.

ylim

numeric(2) vector of length 2 specifying m/z range. If NULL (default), uses full m/z range.

border

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

fill

Color for peak rectangle fills (default: NA for no fill).

msLevel

integer(1) specifying MS level (default: 1).

Value

A ggplot object showing chromatographic peaks as rectangles in retention time vs. m/z space.

Details

The function:

• Plots each peak as a rectangle spanning its rt and m/z ranges

• Uses geom_rect to create the peak rectangles

• Supports interactive plotting through plotly conversion

See also

xcms::plotChromPeaks() for the original xcms implementation

Author

Jan Stanstrup

Examples

library(xcmsVis)
library(xcms)
library(faahKO)
library(MsExperiment)
library(BiocParallel)

# Load example data
cdf_files <- dir(system.file("cdf", package = "faahKO"),
                 recursive = TRUE, full.names = TRUE)[1:3]

# Create XcmsExperiment and perform peak detection
xdata <- readMsExperiment(spectraFiles = cdf_files, BPPARAM = SerialParam())
cwp <- CentWaveParam(peakwidth = c(20, 80), ppm = 25)
xdata <- findChromPeaks(xdata, param = cwp, BPPARAM = SerialParam())

# Create plot
p <- gplotChromPeaks(xdata, file = 1)
print(p)