Plot HCA Results of a Spectra Object

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.

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.

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/

Author

Bryan A. Hanson (DePauw University).

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)
}