CODEWITHSUNDEEP
rggplot2dendrogramphylogenydendextend
echo
echo

Reputation: 11

Positioning tip labels next to the tips in the dendrogram

I read in a tree (.nex), convert it to dendro class, and plot it using ggdendrogram from ggplot2. How can I position the tip labels next to the tips in the dendrogram and not at the bottom?

mytree <- read.nexus('mytree.nex')
den_data_mytree <- dendro_data(as.dendrogram(mytree))
pdf('mytree.pdf', h=55,w=55)
ggdendrogram(den_data_mytree, theme_dendro=F, labels=F) +
  labs(x = "x label", y = "y label", title = "Title") + 
  geom_text(data = den_data_mytree$labels, aes(x, y, label = label,color=den_data_mytree$labels$group), hjust = 1.2, size = 9, angle=90) + 
  scale_colour_manual(values=c("purple","orange")) +
  theme(axis.text=element_text(size=24), axis.title=element_text(size=54,face="bold"), title = element_text(size=54), legend.title = element_blank())
dev.off()

The output is this image:

ggdendogram

Here is the data:

>dput(core_snp_tree)
structure(list(edge = structure(c(109L, ..., 108L), .Dim = c(213L, 2L)), edge.length = c(0.00373, 0,  3e-05, ..., 0.00844), Nnode = 106L,      node.label = c("", "100.00", ..., "100.00"), tip.label = c("list","of","tip","labels"), root.edge = 0), class = "phylo", order = "cladewise")

Upvotes: 1

Views: 585

Answers (1)

Tal Galili
Tal Galili

Reputation: 25306

You'd probably want to use the dendextend package, with the hang.dendrogram function together with ggdend (the simplest way is to use ggplot call on the dendrogram object). In general, dendextend::ggdend is a more extended version of ggdendro.

Example:

hc <- hclust(dist(USArrests[1:5, ]), "ave")
library(dendextend)
dend <- hang.dendrogram(as.dendrogram(hc))
library(ggplot2)
ggplot(dend)

enter image description here

For more details, see here.

Upvotes: 1

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