plotAlignmentPath: Visualize alignment path through similarity matrix
In Roestlab/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms
Description
Usage
Arguments
Value
Author(s)
Examples
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
1
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
1
2
3
4
5
6
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)
Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.
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Description Usage Arguments Value Author(s) Examples
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
1 | 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
1 2 3 4 5 6 | 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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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