hcaScores {ChemoSpecUtils}  R Documentation 
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.
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 lowercase 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") }