ChemoSpecUtils (version 1.0.4)

hcaScores: HCA on PCA/MIA/PARAFAC scores from a Spectra or Spectra2D Object

Description

A wrapper which performs HCA on the scores from a PCA of a Spectra object or POP/MIA/PARAFAC of a Spectra2D object. Many methods for computing the clusters and distances are available.

Usage

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

Value

A list, containing an object of class hclust and an object of class dendrogram. The side effect is a plot.

Arguments

spectra

An object of S3 class ChemoSpec::Spectra() or ChemoSpec2D::Spectra2D().

so

"Score Object" One of the following:

• An object of class prcomp, created by ChemoSpec functions c_pcaSpectra, r_pcaSpectra, irlba_pcaSpectra or s_pcaSpectra.

• An object of class mia produced by function miaSpectra2D.

• An object of class parafac produced by function pfacSpectra2D.

• An object of class pop produced by function popSpectra2D.

Any of the above score objects will have been modified to include a list element called $method, a character string describing the pre-processing carried out and the type of PCA performed (used to annotate the plot).

scores

A vector of integers specifying the components (scores) to plot.

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. Applies only to Spectra objects.

leg.loc

Character; if "none" no legend will be drawn. Otherwise, any string acceptable to legend.

...

Parameters to be passed to the plotting routines. Applies to base graphics only.

Author

Bryan A. Hanson (DePauw University).

See Also

hclust for the underlying function. See hcaSpectra for HCA of the entire data set stored in the Spectra object.

Examples

if (checkForPackageWithVersion("ChemoSpec", 6.0)) {
  library("ChemoSpec")
  data(metMUD1)

  pca <- c_pcaSpectra(metMUD1)
  hca <- hcaScores(metMUD1, pca, main = "metMUD1 NMR Data PCA Scores")
}

if (checkForPackageWithVersion("ChemoSpec2D", 0.5)) {
  library("ChemoSpec2D")
  data(MUD1)

  mia <- miaSpectra2D(MUD1)
  hca <- hcaScores(MUD1, mia, scores = 1:2, main = "MUD1 MIA Scores")

  set.seed(123)
  pfac <- pfacSpectra2D(MUD1, parallel = FALSE, nfac = 2)
  hca <- hcaScores(MUD1, pfac, scores = 1:2, main = "MUD1 PARAFAC Scores")
}