Comparison of the methods of `hclust`

hclust_hull.R

library(dplyr)
library(ggplot2)
x <- c("ward.D","ward.D2", "single","complete",
       "average","mcquitty","median","centroid")

X <- log(as.matrix(iris[,1:2]))

df <- data.frame(X)

d <- dist(X)
dm <- as.matrix(d)
hres <- lapply(x, function(m)hclust(d, method=m))

do <- lapply(1:length(x),
             function(i){data.frame(
               X,
               cl2=cutree(hres[[i]],k=3),
               cl3=cutree(hres[[i]],k=4),
               method=x[i])})

df <-bind_rows(do) %>% 
  mutate(method=factor(method,levels=x))
head(df)

hull <- group_by(df, method, cl3) %>% 
  slice(chull(Sepal.Length, Sepal.Width))

ggplot(df,aes(x=Sepal.Length, y=Sepal.Width))+
  geom_polygon(data=hull, aes(group=cl3), 
               colour="grey40",
               linetype=1,
               fill=NA)+
  geom_point(aes(colour=factor(cl2)), alpha=0.5)+
  facet_wrap(~method)+
  theme_bw()+labs(colour="cluster")
ggsave("hull.png")