ChemoSpec: hcaSpectra – R documentation

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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.

Author(s)

Bryan A. Hanson, DePauw University.

Examples

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

ChemoSpec

Exploratory Chemometrics for Spectroscopy

v5.3.11

GPL-3

Authors

Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>), Mike Bostock [cph, ctb] (author of the d3.js library used by plotSpectraJS, http://d3js.org), Matt Keinsley [ctb] (author of initial AOV-PCA code)

Initial release

2021-03-24