ChemoSpec (version 6.1.10)

hcaSpectra: 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",
  ...
)

Value

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

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.

Author

Bryan A. Hanson (DePauw University).

See Also

hclust for the underlying function. hcaScores for similar analysis of PCA scores from a Spectra object. Additional documentation at https://bryanhanson.github.io/ChemoSpec/

Examples

# You need to install package "amap" for this example
if (requireNamespace("amap", quietly = TRUE)) {
  data(SrE.IR)
  myt <- expression(bolditalic(Serenoa) ~ bolditalic(repens) ~ bold(IR ~ Spectra))
  res <- hcaSpectra(SrE.IR, main = myt)
}