MDSplot: Multidimensional scaling of spectral similarity data

In CluMSID: Clustering of MS2 Spectra for Metabolite Identification

Description

MDSplot() is used to generate multidimensional scaling plots from spectral similarity data. An interactive visualisation can be produced using plotly.

Usage

MDSplot(distmat, interactive = FALSE, highlight_annotated = FALSE, ...)

Arguments

distmat	A distance matrix as generated by distanceMatrix.
interactive	Logical, defaults to FALSE. If TRUE, an interactive visualisation is generated using plotly.
highlight_annotated	Logical, defaults to FALSE. If TRUE, points for features for which an annotation was added before using distanceMatrix are highlighted by red colour, while other points are grey in the MDS plot.
...	Additional arguments passed to geom_point(), e.g. pch, size or alpha.

Value

An MDS plot generated with the help of cmdscale, ggplot and, if interactive, ggplotly.

Examples

load(file = system.file("extdata",
    "distmat.RData",
    package = "CluMSIDdata"))

MDSplot(distmat, highlight_annotated = TRUE)

CluMSID documentation built on Nov. 8, 2020, 7:46 p.m.