getAlignedFigs {DIAlignR} | R Documentation

## 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, 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)
    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)

[Package DIAlignR version 1.2.0 Index]