man/plotAlignmentPath.Rd
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 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/visualise_chromatograms.R
 \name{plotAlignmentPath}
 \alias{plotAlignmentPath}
 \title{Visualize alignment path through similarity matrix}
 \usage{
 plotAlignmentPath(AlignObjOutput)
 }
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 \arguments{
 \item{AlignObjOutput}{(list) The list contains AlignObj, raw XICs for reference and experiment, and reference-peak label.}
 }
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 \value{
 A plot to the current device.
 }
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 \description{
 Plot aligned path through the similarity matrix. Reference run has indices on X-axis, eXp run has them on Y-axis.
 In getAlignObjs function, objType must be set to medium.
 }
 \examples{
 library(lattice)
 dataPath <- system.file("extdata", package = "DIAlignR")
 runs <- c("hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt",
  "hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt")
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 AlignObjOutput <- getAlignObjs(analytes = 4618L, runs, dataPath = dataPath, objType = "medium")
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 plotAlignmentPath(AlignObjOutput)
 }
 \author{
 Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
 
 ORCID: 0000-0003-3500-8152
 
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 License: (c) Author (2019) + GPL-3
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 Date: 2019-12-13
 }