Get MS2 match plots from a metIdentifyClass object. Maturing lifecycle

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).

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])
#> Warning: Removed 26 rows containing missing values (geom_segment).
#> Warning: Removed 8 rows containing missing values (geom_segment).