R: HCA on PCA scores from a Spectra Object

hcaScores {ChemoSpec}

R Documentation

HCA on PCA scores from a Spectra Object

Description

A wrapper which performs HCA on the scores from a PCA of a Spectra object, color-coding the results as specified in the object. Many methods for computing the clusters and distances are available.

Usage

hcaScores(spectra, pca, scores = c(1:5), c.method = "complete",
  d.method = "euclidean", use.sym = FALSE, leg.loc = "topright", ...)

Arguments

`spectra`	An object of S3 class `Spectra`.
`pca`	An object of class `prcomp`, modified to include a list element called `$method`, a character string describing the pre-processing carried out and the type of PCA performed (it appears on the plot). This is automatically provided if `ChemoSpec` functions `c_pcaSpectra` or `r_pcaSpectra` were used to create `pca`.
`scores`	A vector of integers specifying which scores to use for the HCA.
`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`.
`...`	Additional 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.

References

https://github.com/bryanhanson/ChemoSpec

Examples


data(SrE.IR)
pca <- c_pcaSpectra(SrE.IR, choice = "noscale")
myt <- expression(bolditalic(Serenoa)~bolditalic(repens)~bold(IR~Spectra))
res <- hcaScores(SrE.IR,  pca, scores = c(1:5), main = myt)

[Package ChemoSpec version 4.4.97 Index]