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Colored Dendrogram

Description

This is a colored dendrogram. Each cluster have its color. Plus, the plot displays a factor below in order to compare it with the clusters resulting of the tree cut. On the left is shown the evolution of the hubertgamma criterion.

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Requirements

source code

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RGraphGallery(79,12,8)

packages

The following packages will be needed to produce that graph

fpc
A2R

Keywords

bioconductor
Dimension: multivariate
Mathematical annotations
Quantile regression
Rcore: core
Rcore: fonts
system: grid
system: lattice
system: rgl
triplot
Var: circular
Var: factor
Var: numeric
Var: TimeSeries
View: distribution
View: linear relation
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 3D
 bioconductor
 Cluster analysis
 Dimension:
         bivariate
         multivariate
         univariate
 histogram
 Mathematical annotations
 Quantile regression
 Rcore:
         colors
         core
         fonts
 system:
         graphics
         grid
         lattice
         rgl
 triplot
 Var:
         circular
         factor
         numeric
         TimeSeries
 View:
         distribution
         linear relation
         spatial
         trees

See also ...

Wiki page

 Go to the wiki page associated to that graphic. Feel free to add comments, etc ... there.
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Author(s)

Romain Francois 
   
require(fpc) 

require(A2R) 
# get that package from
# http://addictedtor.free.fr/packages


d.usa <- dist(USArrests, "euc") 
h.usa <- hclust(d.usa, method="ward") 

set.seed(1)
some.factor <- letters[1:4][rbinom(50, prob=0.5, size=3)+1] 

hubertgamma <- rep(0,10) 
for(i in 1:10){
  hubertgamma[i] <- cluster.stats(d.usa, 
                                  cutree(h.usa, k=i+1), 
                                  G2 = FALSE,
                                  G3 = FALSE,
                                  silhouette = FALSE)$hubertgamma 
}

A2Rplot(h.usa,
        k=3,
        fact.sup=some.factor, 
        criteria=hubertgamma,
        boxes = FALSE,
        col.up = "gray", 
        col.down = c("orange","royalblue","green3"))