wrTopDownFrag (version 1.0.4)

plotMgfLike: 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
)

Value

This function returns a mgf-like figure

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

See Also

makeFragments, identifVarModif, identifFixedModif, identifyPepFragments

Examples

set.seed(2025)