HCplot: Generate cluster dendrogram or heatmap from spectral...

In tdepke/CluMSID: Clustering of MS2 Spectra for Metabolite Identification

Generate cluster dendrogram or heatmap from spectral similarity data

Description

HCplot() performs hierarchical clustering of spectral similarity data using average linkage as agglomeration criterion like HCtbl and generates either a circular dendrogram or a combination of dendrogram and heatmap.

Usage

HCplot(distmat, h = 0.95, type = c("dendrogram", "heatmap"), ...)

Arguments

distmat	A distance matrix as generated by distanceMatrix.
h	Height where the tree is to be cut, defaults to 0.95. See cutree for details.
type	Specifies which visualisation is to be generated: "dendrogram" (default) for a circular dendrogram or "heatmap" for a combination of dendrogram and heatmap.
...	Additional graphical parameters passed to plot.phylo (for type = "dendrogram") or gplots::heatmap.2 (for type = "heatmap")

Value

A plot as specified by type.

Examples

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

HCplot(distmat[1:50,1:50], h = 0.8, type = "heatmap")

tdepke/CluMSID documentation built on April 10, 2022, noon