Generate MS2 Mirror Plot

This function is used to generate an MS2 mirror plot between two spectra, with the option to highlight reference peaks from a third spectrum.

Usage

plot_ms2_mirror(
  ms2.top,
  ms2.top.id,
  ms2.bot,
  ms2.bot.id,
  ms2.metadata,
  ppm.tolerance = -1,
  da.tolerance = -1,
  add.ref = FALSE,
  ms2.ref = NULL,
  ms2.ref.id = NULL
)

Arguments

ms2.top

Dataframe or matrix containing two columns, mz and intensity, for the top spectrum to be plotted.

ms2.top.id

Numeric MS2 scan identifier for MS2 peaks on the top of the plot.

ms2.bot

Dataframe or matrix containing two columns, mz and intensity, for the bottom spectrum to be plotted.

ms2.bot.id

Numeric MS2 scan identifier for MS2 peaks on the bottom of the plot.

ms2.metadata

Dataframe containing metabolite information including scan.id, name, rt.

ppm.tolerance

Numeric, determines what m/z tolerance will be used in spectral cleaning. Default is -1.

da.tolerance

Numeric, determines what m/z tolerance will be used in spectral cleaning. Default is -1.

add.ref

Boolean, indicates if a third MS2 spectrum is provided for identifying matched peaks present in ms2.top or ms2.bot m/z values. Default is FALSE.

ms2.ref

Dataframe or matrix containing two columns, mz and intensity, for the MS2 spectrum to be used as a third reference. Default is NULL.

ms2.ref.id

Numeric MS2 scan identifier for reference MS2 peaks. Default is NULL.

Value

A ggplot object containing the MS2 mirror plot.

Details

Note: MS2 spectral cleaning is done by msentropy::clean_spectrum(). Therefore, either provide ppm.tolerance or da.tolerance, not both.