peakplot06: A function to plot MS data

In MargaretBaker/plantGlycoMS: A package for processing plant glycosylation MS data

Description

this function plots MS data

Usage

peakplot06(peptideSequence, spec, FUN = defaultIons,
  fi = protViz::fragmentIon(peptideSequence, FUN = FUN)[[1]], main = NULL,
  sub = NULL, xlim = range(spec$mZ, na.rm = TRUE),
  ylim = range(spec$intensity, na.rm = TRUE), itol = 0.06,
  pattern.abc = "[abc].*", pattern.xyz = "[xyz].*", ion.axes = TRUE)

Arguments

peptideSequence	a peptide sequence
spec	a spectrum
FUN	a function to calculate ions, default is defaultIons
fi	a fragment ion function, default is protViz::fragmentIon(peptideSequence, FUN = FUN)[[1]]
main	the main title of a plot, default is NULL
sub	the subtitle of a plot, default is NULL
xlim	the limits of the x axis, default is range(spec$mZ, na.rm = TRUE)
itol	the fragment ion mass tolerance in delta mz, default is 0.02
pattern.abc	the abc pattern, default is "[abc].*"
pattern.xyz	the xyz pattern, default is "[xyz].*", ion.axes = TRUE)
the	limits of the y axis, default is ylim = range(spec$intensity, na.rm = TRUE)

Examples

peakplot06()

MargaretBaker/plantGlycoMS documentation built on May 9, 2019, 9:56 p.m.