HCplot {CluMSID} | R Documentation

## 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")

[Package CluMSID version 1.3.1 Index]