R: Plot HCA Results of a Spectra Object

hcaSpectra {ChemoSpec} | R Documentation

## Plot HCA Results of a Spectra Object

### Description

A wrapper which carries out HCA and plots a dendrogram colored by the information in a `Spectra` object. Many methods for computing the clusters and distances are available.

### Usage

    hcaSpectra(spectra, c.method = "complete", d.method = "euclidean",
      use.sym = FALSE, leg.loc = "topright", ...)

### Arguments

`spectra` | An object of S3 class `Spectra`.
`c.method` | A character string describing the clustering method; must be acceptable to `hclust`.
`d.method` | A character string describing the distance calculation method; must be acceptable as a method in `rowDist`.
`use.sym` | A logical; if true, use no color and use lower-case letters to indicate group membership.
`leg.loc` | Character; if `"none"` no legend will be drawn. Otherwise, any string acceptable to `legend`.
`...` | Other parameters to be passed to the plotting functions.

### Value

A list, containing an object of class `hclust` and an object of class `dendrogram`. The side effect is a plot.

### Author(s)

Bryan A. Hanson, DePauw University.

### References

https://github.com/bryanhanson/ChemoSpec

### See Also

`hclust` for the underlying function. `hcaScores` for similar analysis of PCA scores from a `Spectra` object. `plotHCA` for the function that actually does the plotting.

### Examples

    data(SrE.IR)
    myt <- expression(bolditalic(Serenoa)~bolditalic(repens)~bold(IR~Spectra))
    res <- hcaSpectra(SrE.IR, main = myt)

[Package ChemoSpec version 4.4.97 Index]