plotPrecursorIons: General visualization of precursor ions of LC-MS/MS data

In sneumann/xcms: LC-MS and GC-MS Data Analysis

General visualization of precursor ions of LC-MS/MS data

Description

Simple visualization of the position of fragment spectra's precursor ion in the MS1 retention time by m/z area.

Usage

plotPrecursorIons(
  x,
  pch = 21,
  col = "#00000080",
  bg = "#00000020",
  xlab = "retention time",
  ylab = "m/z",
  main = character(),
  ...
)

Arguments

x	MsExperiment of LC-MS/MS data.
pch	integer(1) defining the symbol/point type to be used to draw points. See points() for details. Defaults to pch = 21 which allows defining the background and border color for points.
col	the color to be used for all data points. Defines the border color if pch = 21.
bg	the background color (if pch = 21).
xlab	character(1) defining the x-axis label.
ylab	character(1) defining the y-axis label.
main	Optional character(1) with the title for every plot. If not provided (the default) the base file name will be used for each sample.
...	additional parameters to be passed to the plot calls.

Author(s)

Johannes Rainer

Examples

## Load a test data file with DDA LC-MS/MS data
library(MsExperiment)
fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
pest_dda <- readMsExperiment(fl)

plotPrecursorIons(pest_dda)
grid()

## Subset the data object to plot the data specifically for one or
## selected file/sample:
plotPrecursorIons(pest_dda[1L])

sneumann/xcms documentation built on June 5, 2024, 4:28 p.m.