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

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 with the title for each plot. If not provided (the default), the row names of sampleData(x) are used. sample.

...

additional parameters to be passed to the plot calls.

Author

Johannes Rainer

Examples

## Load a test data file with DDA LC-MS/MS data
library(MsExperiment)
library(MsDataHub)
fl <- MsDataHub::PestMix1_DDA.mzML()
#> see ?MsDataHub and browseVignettes('MsDataHub') for documentation
#> loading from cache
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])