ChemoSpec (version 4.4.97)

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", ...)

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.

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

# NOT RUN {
data(SrE.IR)
myt <- expression(bolditalic(Serenoa)~bolditalic(repens)~bold(IR~Spectra))
res <- hcaSpectra(SrE.IR, main = myt)

# }