plotAlignedAnalytes: Plot aligned XICs group for a specific peptide....

In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

Plot aligned XICs group for a specific peptide. AlignObjOutput is the output from getAlignObjs fucntion.

Usage

plotAlignedAnalytes(
  AlignObjOutput,
  plotType = "All",
  outFile = "AlignedAnalytes.pdf",
  annotatePeak = FALSE,
  saveFigs = FALSE
)

Arguments

AlignObjOutput	(list) list contains fileInfo, AlignObj, raw XICs for reference and experiment, and reference-peak label.
plotType	(string) must be one of the strings "All", "onlyUnaligned" and "onlyAligned".
outFile	(string) name of the output pdf file.
annotatePeak	(logical) TRUE: Peak boundaries and apex will be highlighted.
saveFigs	(logical) TRUE: Figures will be saved in AlignedAnalytes.pdf .

Value

A plot to the current device.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-13

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt",
 "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt")
AlignObjOutput <- getAlignObjs(analytes = 4618L, runs, dataPath = dataPath)
plotAlignedAnalytes(AlignObjOutput)

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.