Colorize Clusters in Dendogram with ggplot2

dendextend, ggdendro, ggplot2, r

Solution

Workaround would be to plot cluster object with `plot()` and then use function `rect.hclust()` to draw borders around the clusters (nunber of clusters is set with argument `k=`). If result of `rect.hclust()` is saved as object it will make list of observation where each list element contains observations belonging to each cluster.

plot(hc)
gg<-rect.hclust(hc,k=2)

Now this list can be converted to dataframe where column `clust` contains names for clusters (in this example two groups) - names are repeated according to lengths of list elemets.

clust.gr<-data.frame(num=unlist(gg),
  clust=rep(c("Clust1","Clust2"),times=sapply(gg,length)))
head(clust.gr)
      num  clust
sta_1   1 Clust1
sta_2   2 Clust1
sta_3   3 Clust1
sta_5   5 Clust1
sta_8   8 Clust1
sta_9   9 Clust1

New data frame is merged with `label()` information of `dendr` object (`dendro_data()` result).

text.df<-merge(label(dendr),clust.gr,by.x="label",by.y="row.names")
head(text.df)
   label  x y num  clust
1  sta_1  8 0   1 Clust1
2 sta_10 28 0  10 Clust2
3 sta_11 41 0  11 Clust2
4 sta_12 31 0  12 Clust2
5 sta_13 10 0  13 Clust1
6 sta_14 37 0  14 Clust2

When plotting dendrogram use `text.df` to add labels with `geom_text()` and use column `clust` for colors.

ggplot() + 
  geom_segment(data=segment(dendr), aes(x=x, y=y, xend=xend, yend=yend)) + 
  geom_text(data=text.df, aes(x=x, y=y, label=label, hjust=0,color=clust), size=3) +
  coord_flip() + scale_y_reverse(expand=c(0.2, 0)) + 
  theme(axis.line.y=element_blank(),
        axis.ticks.y=element_blank(),
        axis.text.y=element_blank(),
        axis.title.y=element_blank(),
        panel.background=element_rect(fill="white"),
        panel.grid=element_blank())

Problem

Didzis Elferts showed how to plot a dendogram using ggplot2 and ggdendro: horizontal dendrogram in R with labels here is the code: ``` labs = paste("sta_",1:50,sep="") #new labels rownames(USArrests)<-labs #set new row names hc <- hclust(dist(USArrests), "ave") library(ggplot2) library(ggdendro) #convert cluster object to use with ggplot dendr <- dendro_data(hc, type="rectangle") #your own labels are supplied in geom_text() and label=label ggplot() + geom_segment(data=segment(dendr), aes(x=x, y=y, xend=xend, yend=yend)) + geom_text(data=label(dendr), aes(x=x, y=y, label=label, hjust=0), size=3) + coord_flip() + scale_y_reverse(expand=c(0.2, 0)) + theme(axis.line.y=element_blank(), axis.ticks.y=element_blank(), axis.text.y=element_blank(), axis.title.y=element_blank(), panel.background=element_rect(fill="white"), panel.grid=element_blank()) ``` Does anyone know, how to colorize the different clusters? For example, you want to have 2 Clusters (k=2) colorized?

Original source

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