plotAlignedAnalytes {DIAlignR} | 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)

[Package DIAlignR version 1.2.0 Index]