dendextend (version 0.14.2)

color_branches: Color tree's branches according to sub-clusters

Description

This function is for dendrogram and hclust objects. This function colors both the terminal leaves of a tree's cluster and the edges leading to those leaves. The edgePar attribute of nodes will be augmented by a new list item col. The groups will be defined by a call to cutree using the k or h parameters. If col is a color vector with a different length than the number of clusters (k) - then a recycled color vector will be used.

Usage

color_branches(tree, k = NULL, h = NULL, col, groupLabels = NULL, ...)

Arguments

tree

A dendrogram or hclust tree object

k

number of groups (passed to cutree)

h

height at which to cut tree (passed to cutree)

col

Function or vector of Colors. By default it tries to use rainbow_hcl from the colorspace package. (with parameters c=90 and l=50). If colorspace is not available, It will

groupLabels

If TRUE add numeric group label - see Details for options

...

ignored.

Value

• a tree object of class dendrogram.

source

This function is a derived work from the color_clusters function, with some ideas from the slice function - both are from the {dendroextras} package by jefferis. It extends it by using cutree.dendrogram - allowing the function to work for trees that hclust can not handle (unbranched and non-ultrametric trees). Also, it allows REPEATED cluster color assignments to branches on to the same tree. Something which the original function was not able to handle.

Details

If groupLabels=TRUE then numeric group labels will be added to each cluster. If a vector is supplied then these entries will be used as the group labels. If a function is supplied then it will be passed a numeric vector of groups (e.g. 1:5) and must return the formatted group labels. If the labels of the dendrogram are NOT character (but, for example integers) - they are coerced into character. This step is essential for the proper operation of the function. A dendrogram labels might happen to be integers if they are based on an hclust performed on a dist of an object without rownames.

See Also

cutree,dendrogram, hclust, labels_colors

Examples

dend <- as.dendrogram(hclust(dist(USArrests), "ave"))
d1=color_branches(dend,5, col = c(3,1,1,4,1))
plot(d1) # selective coloring of branches :)
d2=color_branches(d1,5)
plot(d2)

d1=color_branches(dend,5, col = c(3,1,1,4,1),groupLabels=TRUE)
plot(d1) # selective coloring of branches :)
d2=color_branches(d1,5,groupLabels=TRUE)
plot(d2)

d5=color_branches(dend,5)
plot(d5)
d5g=color_branches(dend,5,groupLabels=TRUE)
plot(d5g)
d5gr=color_branches(dend,5,groupLabels=as.roman)
plot(d5gr)

# messy - but interesting:
dend_override=color_branches(dend,2,groupLabels=as.roman)
dend_override=color_branches(dend_override,4,groupLabels=as.roman)
dend_override=color_branches(dend_override,7,groupLabels=as.roman)
plot(dend_override)

d5=color_branches(tree=dend[[1]],k=5)


require(dendextend)
data(iris, envir = environment())
d_iris <- dist(iris[,-5])
hc_iris <- hclust(d_iris)
dend_iris <- as.dendrogram(hc_iris)
dend_iris=color_branches(dend_iris,k=3)

labels_colors(dend_iris) <-
 rainbow_hcl(3)[sort_levels_values(
 as.numeric(iris[,5])[order.dendrogram(dend_iris)]
 )]

plot(dend_iris,
main = "Clustered Iris dataset",
 sub = "labels are colored based on the true cluster")



# cutree(dend_iris,k=3, order_clusters_as_data=FALSE,
   # sort_cluster_numbers = TRUE, try_cutree_hclust=FALSE)
# cutree(dend_iris,k=3, order_clusters_as_data=FALSE,
   # sort_cluster_numbers = TRUE, try_cutree_hclust=TRUE)

require(colorspace)

data(iris, envir = environment())
d_iris <- dist(iris[,-5])
hc_iris <- hclust(d_iris)
labels(hc_iris) # no labels, because "iris" has no row names
dend_iris <- as.dendrogram(hc_iris)
is.integer(labels(dend_iris)) # this could cause problems...

iris_species <- rev(levels(iris[,5]))
dend_iris <- color_branches(dend_iris,k=3, groupLabels=iris_species)
is.character(labels(dend_iris)) # labels are no longer "integer"

# have the labels match the real classification of the flowers:
labels_colors(dend_iris) <-
   rainbow_hcl(3)[sort_levels_values(
      as.numeric(iris[,5])[order.dendrogram(dend_iris)]
   )]

# We'll add the flower type
labels(dend_iris) <- paste(as.character(iris[,5])[order.dendrogram(dend_iris)],
                           "(",labels(dend_iris),")",
                           sep = "")

dend_iris <- hang.dendrogram(dend_iris,hang_height=0.1)

# reduce the size of the labels:
dend_iris <- assign_values_to_leaves_nodePar(dend_iris, 0.5, "lab.cex")

par(mar = c(3,3,3,7))
plot(dend_iris,
     main = "Clustered Iris dataset
     (the labels give the true flower species)",
     horiz =  TRUE,  nodePar = list(cex = .007))
legend("topleft", legend = iris_species, fill = rainbow_hcl(3))
a= dend_iris[[1]]
dend_iris1 <- color_branches(a,k = 3)
plot(dend_iris1)

# str(dendrapply(d2, unclass))
# unclass(d1)