plotMgfLike: Draw simplified (deconvoluted) spectrum of mgf type and...

In wrTopDownFrag: Internal Fragment Identification from Top-Down Mass Spectrometry

Draw simplified (deconvoluted) spectrum of mgf type and highlight peaks with matches found to theoretical data

Description

Draw simplified (deconvoluted) spectrum of mgf type and highlight matches found

Usage

plotMgfLike(
  lst,
  basInp = NULL,
  backgrCol = NULL,
  replNames = c("by", "i"),
  lwd = 1,
  col = NULL,
  tit = NULL,
  xLim = NULL,
  yLab = NULL,
  linPlot = FALSE,
  listNa = c("identif", "overview", "obsMass"),
  useColN = c("obsMass", "logInt", "origNa", "mod", "modSpec", "fraNa", "orig",
    "nIdentif", "minMassDec", "maxMass"),
  cex = 1,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

lst	(list) result of identificationi with element $obsMass (the column 'obsMass' should be m/z values, the column 'sc.logInt' intensity values) and $identif
basInp	(numeric) alternative/custom entry of observaed masses
backgrCol	(character) color of background
replNames	(character)
lwd	(numeric) line width
col	(character) custom colors for different types of ions/modifications
tit	(character) custom title
xLim	(numeric length=2) custom x axis margins
yLab	(character) custom y axis label
linPlot	(logical) re-transform y-axis from log2 to linear scale
listNa	(character) list-elements of 'lst' to use/extract
useColN	(character) columns names tu use from input ie lst$identif & lst$overview
cex	(numeric) expansion factor for x- and y-label
silent	(logical) suppress messages
debug	(logical) additional messages for debugging
callFrom	(character) allows easier tracking of messages produced

Value

This function returns a mgf-like figure

See Also

makeFragments, identifVarModif, identifFixedModif, identifyPepFragments

Examples

set.seed(2025)

wrTopDownFrag documentation built on June 8, 2025, 1:34 p.m.