plotAlignedAnalytes: Plot aligned XICs group for a specific peptide....
In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

View source: R/visualise_chromatograms.R

plotAlignedAnalytes

R Documentation

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

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, shubh.gupta@mail.utoronto.ca

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)

shubham1637/DIAlignR documentation built on March 29, 2023, 8:45 p.m.