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

In CluMSID: Clustering of MS2 Spectra for Metabolite Identification

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")

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