getAlignedFigs: Plot aligned XICs group for a specific peptide.

In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Plot aligned XICs group for a specific peptide.

Description

AlignObj is the output from getAlignObjs fucntion. This function prepares ggplot objects from AlignObj.

Usage

getAlignedFigs(
  AlignObj,
  XICs.ref,
  XICs.eXp,
  refPeakLabel,
  annotatePeak = FALSE
)

Arguments

AlignObj	(S4 object)
XICs.ref	(list) List of extracted ion chromatograms (dataframe) from reference run. The dataframe has two columns: first column is for time and second column indicates intensity.
XICs.eXp	(list) List of extracted ion chromatograms (dataframe) from experiment run.The dataframe has two columns: first column is for time and second column indicates intensity.
refPeakLabel	(numeric vector) It contains peak apex, left width and right width.
annotatePeak	(logical) TRUE: Peak boundaries and apex will be highlighted.

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)
AlignObj <- AlignObjOutput[[2]][["4618"]][[1]][["AlignObj"]]
XICs.ref <- AlignObjOutput[[2]][["4618"]][[1]][["ref"]]
XICs.eXp <- AlignObjOutput[[2]][["4618"]][[1]][["eXp"]]
refPeakLabel <- AlignObjOutput[[2]][["4618"]][[1]][["peak"]]
## Not run: 
getAlignedFigs(AlignObj, XICs.ref, XICs.eXp, refPeakLabel)

## End(Not run)

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