树状图的分​​层聚类的不同可视化

Question

I would like to have visualization of hierarchical clustering with shapes one inside the other. Brightness level represents level of hierarchy. Let me show you my idea with an example:

# Clustering small proportion of iris data   
clusters <- hclust(dist(iris[20:28, 3:4]), method = 'average')
# Visualizing the result as a dendogram    
plot(clusters)

Now we can convert the dendrogram as below.

Is there any R package that can produce something similar?

Answer 1

This is only a partial answer. You can use clusplot from the cluster package to get some way in that direction. You could probably improve on this by changing the source of clusplot (type getAnywhere(clusplot.default) to get the source). But it is probably some work to get your bubbles to not overlap. Anyway, here's the plot you get from clusplot . It may also be of interest to look at the individual plots one at a time instead of showing them all together.

# use sample data
df <- iris[20:28, 3:4]
# calculate hierarchical clustering
hfit <- hclust(dist(df), method = 'average')
# plot dendogram
plot(hfit)
# use clusplot at all possible cutoffs and show on top of each other.
library(cluster)
clusplot(df, cutree(hfit, 1), lines = 0)
for (i in 2:nrow(df)){
  clusplot(df, cutree(hfit, i), lines = 0, add = TRUE)
}