ggplot2 Version of plotChromPeakImage()

Creates an image/heatmap showing the number of detected chromatographic peaks per sample across retention time bins. This is a ggplot2 implementation of xcms's xcms::plotChromPeakImage() function.

Usage

gplotChromPeakImage(
  object,
  binSize = 30,
  xlim = NULL,
  log_transform = FALSE,
  msLevel = 1L
)

# S4 method for class 'XCMSnExp'
gplotChromPeakImage(
  object,
  binSize = 30,
  xlim = NULL,
  log_transform = FALSE,
  msLevel = 1L
)

# S4 method for class 'XcmsExperiment'
gplotChromPeakImage(
  object,
  binSize = 30,
  xlim = NULL,
  log_transform = FALSE,
  msLevel = 1L
)

Arguments

object

An XCMSnExp or XcmsExperiment object with detected chromatographic peaks.

binSize

numeric(1) value specifying the bin size in seconds for the retention time axis (default: 30).

xlim

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

log_transform

logical(1), whether to log2-transform the peak counts (default: FALSE).

msLevel

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

Value

A ggplot object showing peak counts as a heatmap with retention time on x-axis, samples on y-axis, and color representing peak density.

Details

The function:

• Bins peaks across retention time using specified bin size

• Counts peaks per sample per bin

• Creates heatmap with color representing peak density

• Optionally applies log2 transformation to counts

See also

xcms::plotChromPeakImage() 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 <- gplotChromPeakImage(xdata, binSize = 30)
print(p)