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[Fix] In tandem with the current version of getAlignObjs

shubham1637 authored on 18/04/2020 00:51:30
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@@ -21,8 +21,7 @@ library(lattice)
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 dataPath <- system.file("extdata", package = "DIAlignR")
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 runs <- c("hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt",
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  "hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt")
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-AlignObjOutput <- getAlignObjs(analytes = "QFNNTDIVLLEDFQK_3", runs, dataPath = dataPath,
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- objType = "medium")
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+AlignObjOutput <- getAlignObjs(analytes = 4618L, runs, dataPath = dataPath, objType = "medium")
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 plotAlignmentPath(AlignObjOutput)
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 }
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 \author{
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[Doc] Used devtools::document() to reflect changes from R files to man/ pages

shubham1637 authored on 04/02/2020 16:29:02
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@@ -30,6 +30,6 @@ Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
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 ORCID: 0000-0003-3500-8152
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-License: (c) Author (2019) + MIT
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+License: (c) Author (2019) + GPL-3
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 Date: 2019-12-13
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 }
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[Bioc] return is set as A plot to the current device

shubham1637 authored on 18/12/2019 20:39:38
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@@ -9,6 +9,9 @@ plotAlignmentPath(AlignObjOutput)
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 \arguments{
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 \item{AlignObjOutput}{(list) The list contains AlignObj, raw XICs for reference and experiment, and reference-peak label.}
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 }
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+\value{
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+A plot to the current device.
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+}
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 \description{
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 Plot aligned path through the similarity matrix. Reference run has indices on X-axis, eXp run has them on Y-axis.
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 In getAlignObjs function, objType must be set to medium.
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[Doc] Completed documentation of visualise_chromatogram.R

shubham1637 authored on 17/12/2019 18:01:51
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@@ -6,6 +6,9 @@
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 \usage{
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 plotAlignmentPath(AlignObjOutput)
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 }
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+\arguments{
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+\item{AlignObjOutput}{(list) The list contains AlignObj, raw XICs for reference and experiment, and reference-peak label.}
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+}
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 \description{
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 Plot aligned path through the similarity matrix. Reference run has indices on X-axis, eXp run has them on Y-axis.
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 In getAlignObjs function, objType must be set to medium.
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[Fix] corrected the spelling mistake for plotAlignmentPath

shubham1637 authored on 16/12/2019 16:27:20
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new file mode 100644
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@@ -0,0 +1,29 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/visualise_chromatograms.R
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+\name{plotAlignmentPath}
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+\alias{plotAlignmentPath}
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+\title{Visualize alignment path through similarity matrix}
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+\usage{
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+plotAlignmentPath(AlignObjOutput)
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+}
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+\description{
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+Plot aligned path through the similarity matrix. Reference run has indices on X-axis, eXp run has them on Y-axis.
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+In getAlignObjs function, objType must be set to medium.
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+}
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+\examples{
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+library(lattice)
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+dataPath <- system.file("extdata", package = "DIAlignR")
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+runs <- c("hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt",
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+ "hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt")
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+AlignObjOutput <- getAlignObjs(analytes = "QFNNTDIVLLEDFQK_3", runs, dataPath = dataPath,
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+ objType = "medium")
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+plotAlignmentPath(AlignObjOutput)
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+}
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+\author{
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+Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
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+
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+ORCID: 0000-0003-3500-8152
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+
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+License: (c) Author (2019) + MIT
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+Date: 2019-12-13
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+}