Get MS2 match plots from a metIdentifyClass object.
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
)A metIdentifyClass object.
Used database (databaseClass).
Peak name(s) or "all". You can use which_has_identification functions to get what peaks have identifications.
MS2 fragment match ppm.
The threshold for m/z error calculation.
Work directory.
The width of MS2 spectra match figure (inch).
The height of MS2 spectra match figure (inch).
Output interactive plot or not.
m/z range for MS2 spectra match plot.
Relative intensity range.
Title of x axis.
Title of y axis.
Colour of database MS2 spectrum.
Colour of experimental MS2 spectrum.
Font size of title.
Font size of title of axis.
Font size of axis text.
Legend title size.
Legend text size.
"pdf" or "png".
The number of threads
Output all figure in one folder or not.
Show plot or just save them.
A or all ms2 match plot(s).
The example and demo data of this function can be found https://tidymass.github.io/metid/articles/metid.html