ms2plot: Get MS2 match plots from a metIdentifyClass object

In jaspershen/metID: Metabolite identification based on MS1 and MS2 spectra

Get MS2 match plots from a metIdentifyClass object

Description

Get MS2 match plots from a metIdentifyClass object. \lifecyclematuring

Usage

ms2plot(
  object,
  database,
  which.peak = "all",
  ppm.tol = 30,
  mz.ppm.thr = 400,
  path = ".",
  width = 20,
  height = 8,
  interaction.plot = FALSE,
  range.mz,
  range.int = c(-1, 1),
  xlab = "Mass to charge ratio (m/z)",
  ylab = "Relative intensity",
  col.lib = "red",
  col.exp = "black",
  title.size = 15,
  lab.size = 12,
  axis.text.size = 12,
  legend.title.size = 12,
  legend.text.size = 10,
  figure.type = c("png", "pdf"),
  threads = 3,
  one.folder = TRUE,
  show.plot = TRUE
)

Arguments

object	A metIdentifyClass object.
database	Used database (databaseClass).
which.peak	Peak name(s) or "all". You can use which_has_identification functions to get what peaks have identifications.
ppm.tol	MS2 fragment match ppm.
mz.ppm.thr	The threshold for m/z error calculation.
path	Work directory.
width	The width of MS2 spectra match figure (inch).
height	The height of MS2 spectra match figure (inch).
interaction.plot	Output interactive plot or not.
range.mz	m/z range for MS2 spectra match plot.
range.int	Relative intensity range.
xlab	Title of x axis.
ylab	Title of y axis.
col.lib	Colour of database MS2 spectrum.
col.exp	Colour of experimental MS2 spectrum.
title.size	Font size of title.
lab.size	Font size of title of axis.
axis.text.size	Font size of axis text.
legend.title.size	Legend title size.
legend.text.size	Legend text size.
figure.type	"pdf" or "png".
threads	The number of threads
one.folder	Output all figure in one folder or not.
show.plot	Show plot or just save them.

Value

A or all ms2 match plot(s).

Author(s)

Xiaotao Shen [e-mail]

See Also

The example and demo data of this function can be found https://jaspershen.github.io/metID/articles/metID.html

Examples

data("annotate_result", package = "metID")
data("msDatabase_hilic0.0.2", package = "metID")
peak_name <- which_has_identification(annotate_result)
ms2plot(annotate_result, database = msDatabase_rplc0.0.2, which.peak = peak_name[1,1])

jaspershen/metID documentation built on July 31, 2022, 11:31 p.m.