plotAlignmentPath: Visualize alignment path through similarity matrix
In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

View source: R/visualise_chromatograms.R

plotAlignmentPath

R Documentation

Visualize alignment path through similarity matrix

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.

Usage

plotAlignmentPath(AlignObjOutput)

Arguments

AlignObjOutput

(list) The list contains AlignObj, raw XICs for reference and experiment, and reference-peak label.

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

library(lattice)
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, objType = "medium")
plotAlignmentPath(AlignObjOutput)

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