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ggplot2 Version of plot() for MsExperiment, XcmsExperiment and XCMSnExp

Source: R/gplot-XcmsExperiment-methods.R
gplot-XcmsExperiment.Rd

Creates a two-panel visualization of MS data showing:

  • Upper panel: Base Peak Intensity (BPI) chromatogram vs retention time

  • Lower panel: m/z vs retention time scatter plot with intensity-based coloring

This is a ggplot2 implementation of xcms's plot() method for MsExperiment objects, enabling modern visualization and interactive plotting capabilities.

Usage

# S4 method for class 'XcmsExperiment'
gplot(
  x,
  msLevel = 1L,
  peakCol = "#ff000060",
  col = "grey",
  colramp = grDevices::topo.colors,
  pch = 21,
  ...
)

# S4 method for class 'MsExperiment'
gplot(
  x,
  msLevel = 1L,
  col = "grey",
  colramp = grDevices::topo.colors,
  pch = 21,
  ...
)

# S4 method for class 'XCMSnExp'
gplot(
  x,
  msLevel = 1L,
  peakCol = "#ff000060",
  col = "grey",
  colramp = grDevices::topo.colors,
  pch = 21,
  ...
)

Arguments

x

MsExperiment, XcmsExperiment or XCMSnExp object

msLevel

integer(1) defining the MS level to visualize (default: 1)

peakCol

character(1) color to indicate identified chromatographic peaks (default: "#ff000060")

col

character(1) color for point borders (default: "grey")

colramp

function color ramp for intensity mapping (default: grDevices::topo.colors)

pch

integer(1) point shape (default: 21 = filled circle)

...

additional arguments (for compatibility)

Value

A ggplot or patchwork object showing the two-panel visualization. For single samples, returns a patchwork object with two panels. For multiple samples, returns a patchwork object with all sample plots stacked. Use + labs() to customize axis labels and titles.

Details

The function:

  • Extracts spectra data filtered by MS level

  • Applies adjusted retention times if available

  • Upper panel: plots BPI (max intensity per retention time) with intensity-colored points

  • Lower panel: plots m/z vs retention time scatter with intensity-colored points

  • Overlays detected chromatographic peaks as rectangles (if available)

  • Uses consistent color scale across both panels based on intensity

See also

plot,MsExperiment,missing-method for the original xcms implementation

Examples

library(xcmsVis)
library(xcms)
library(MsExperiment)

# Load and filter data
xmse <- loadXcmsData()
xmse <- filterRt(xmse, rt = c(2620, 2740)) |>
        filterMzRange(mz = c(342, 344))
#> Filter spectra
#> Filter spectra

# Plot MS data
gplot(xmse[1L])


# Multiple samples
gplot(xmse[1:3])