R. Change the leaf size in phylogenic dendogram plot

Question

I am trying to make a phylogenic dendogram plot in R. I used the following code to get pretty much what I am after:

library(igraph)
library(proxy)
library(factoextra)

hc = hclust(dist(mtcars))
dend <- as.dendrogram(hc)

fviz_dend(dend, k = 5,
      repel = TRUE, 
      type ="phylogenic", show_labels=T)

Now though, I would like to increase the size of the individual points. As per the package dendextend, I tried adding leaves_cex in two different ways, as below, both with no success (outcomes explained in code, below).

library(dendextend)
fviz_dend(dend, k = 5,
      repel = TRUE, leaves_cex=50,  # circle size is unchanged
      type ="phylogenic", show_labels=T) 

dend <- as.dendrogram(hc,type ="phylogenic") %>%
  set("leaves_cex", 50) %>% #creates a rectangular dendogram, phylogenic layout lost
  plot()

I can also try using the ape package, as below. Here I can specify the colours, with tip.color, but there is no variable for tip size/shape. Here, the layout is also not as nice as in the original plot above.

library(ape)
clus5 = cutree(hc, 5)
plot(as.phylo(hc),type="unrooted", tip.color = clus5 )

How can I change the leaf marker appearance for properties other than colour?

Answer 1

Using the package ape , the leaves appearance are pretty easy to modify by plotting them separately using the tiplabels function:

## The tree
my_tree <- as.phylo(hc)

## The plot without the tips
plot(my_tree,type = "unrooted", show.tip.label = FALSE)

## The tips (leaves) plotted separately with many options
tiplabels(my_tree$tip.label,
          col = clus5, # Some colours
          cex = 0.5, # The size
          adj = -1, # Position adjustment
          bg = "orange", # A background colour
          frame = "circle" # Some circles
          ) #... Many more options

You can have a look at the ?tiplabels for more info and options.