FactoMineR/factoextra visualize all the clusters in the dendrogram

Question

I performed a hierarchical clustering on a dataframe using the HCPC function of the package FactoMineR. Problem is, I cannot visualize the number of clusters I asked when I draw the dendrogram using factoextra. Here is below a reproducible example of my problem

model <- HCPC(iris[,1:4], nb.clust = 5) 

there are indeed 5 clusters above

fviz_dend(model, k = 5,
          cex = 0.7,                     
          palette = "default",              
          rect = TRUE, rect_fill = TRUE, 
)

But just 3 mapped within the dendrogram

Answer 1

I bumped into the same problem: the fviz_dend function would always return what it considers to be the optimal amount of clusters, even when I tried to override this – either in the HCPC or in the fviz_dend functions.

One way to fix this while sticking to FactoMineR and factoextra would be to change the default amount of clusters calculated by the HCPC function:

model$call$t$nb.clust = 5

And then run the fviz_dend function.

This should return the result that you were expecting.

Answer 2

You can just use the dendextend R package with the color_branches function:

library(dendextend)
dend <- USArrests %>% dist %>% hclust(method = "ave") %>% as.dendrogram
dd <- color_branches(dend,5)
plot(dd)