hcaSpectra: Plot HCA Results of a Spectra Object

In ChemoSpec: Exploratory Chemometrics for Spectroscopy

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).

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)
}

ChemoSpec documentation built on April 15, 2025, 5:09 p.m.