MDSplot: Multidimensional scaling of spectral similarity data

Description Usage Arguments Value Examples

View source: R/distancematrix_mds.R

Description

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

Usage

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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

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

MDSplot(distmat, highlight_annotated = TRUE)

CluMSID documentation built on April 29, 2020, 5:20 a.m.