HCA on PCA/MIA/PARAFAC scores from a Spectra or Spectra2D Object
hcaScores( spectra, so, scores = c(1:5), c.method = "complete", d.method = "euclidean", use.sym = FALSE, leg.loc = "topright", ... )
spectra |
|
so |
"Score Object" One of the following:
Any of the above score objects will have been modified to include a
list element called |
scores |
A vector of integers specifying the components (scores) to plot. |
c.method |
A character string describing the clustering method; must be
acceptable to |
d.method |
A character string describing the distance calculation
method; must be acceptable as a method in |
use.sym |
A logical; if true, use no color and use lower-case letters
to indicate group membership. Applies only to |
leg.loc |
Character; if |
... |
Additional parameters to be passed to the plotting functions. |
A list, containing an object of class hclust and an
object of class dendrogram. The side effect is a plot.
Bryan A. Hanson, DePauw University.
hclust for the underlying function. See
hcaSpectra for HCA of the entire data set stored in the
Spectra object.
if (checkForPackageWithVersion("ChemoSpec", "5.1")) {
library("ChemoSpec")
data(metMUD1)
pca <- c_pcaSpectra(metMUD1)
hca <- hcaScores(metMUD1, pca, main = "metMUD1 NMR Data PCA Scores")
}
if (checkForPackageWithVersion("ChemoSpec2D", "0.3")) {
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")
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