dendextend (version 1.13.4)

get_subdendrograms: Extract a list of k subdendrograms from a given dendrogram object

Description

Extracts a list of subdendrogram structures based on the cutree cutree.dendrogram function from a given dendrogram object. It can be useful in case of more exact visual investigation of clustering results.

Usage

get_subdendrograms(dend, k, ...)

Arguments

dend

a dendrogram object

k

the number of subdendrograms that should be extracted

...

parameters that should be passed to the cutree cutree.dendrogram

Value

A list of k subdendrograms, based on the cutree cutree.dendrogram clustering clusters.

Examples

# NOT RUN {
# needed packages:
# install.packages(gplots)
# install.packages(viridis)
# install.packages(devtools)
# devtools::install_github('talgalili/dendextend') #' dendextend from github

# define dendrogram object to play with:
dend <- iris[, -5] %>%
  dist() %>%
  hclust() %>%
  as.dendrogram() %>%
  set("labels_to_character") %>%
  color_branches(k = 5)
dend_list <- get_subdendrograms(dend, 5)

# Plotting the result
par(mfrow = c(2, 3))
plot(dend, main = "Original dendrogram")
sapply(dend_list, plot)

# plot a heatmap of only one of the sub dendrograms
par(mfrow = c(1, 1))
library(gplots)
sub_dend <- dend_list[[1]] #' get the sub dendrogram
# make sure of the size of the dend
nleaves(sub_dend)
length(order.dendrogram(sub_dend))
# get the subset of the data
subset_iris <- as.matrix(iris[order.dendrogram(sub_dend), -5])
# update the dendrogram's internal order so to not cause an error in heatmap.2
order.dendrogram(sub_dend) <- rank(order.dendrogram(sub_dend))
heatmap.2(subset_iris, Rowv = sub_dend, trace = "none", col = viridis::viridis(100))
# }