I think that what you are asking is "how can I decide on the labels in a dendrogram". So this has two parts. For example, let's use the simple data of the numbers c(1,2,5,6)
1) When you create the hclust using dist, it uses the names of the items. And if they don't exist then it uses a running index. For example:
x <- c(1,2,5,6)
d1 <- as.dendrogram(hclust(dist(x)))
plot(d1)
This is obviously a problem since the items we have are 1,2,5,6 and not 1:4! So how can we fix this? One way is update the names. For example:
x <- c(1,2,5,6)
names(x) <- x
x
d2 <- as.dendrogram(hclust(dist(x)))
plot(d2)
I believe this basically solves your problem (and frankly, doesn't require dendextend). But if you want to update the text AFTER creating the dendrogram - read on:
2)
The dendextend package allows you to update the labels of a dendrogram. But you need to make sure you are using the correct order (since the order of the original vector, and that of the labels in the tree are not the same!). Here is how it can be done:
if (!require(dendextend)) install.packages(dendextend);
library(dendextend)
x <- c(1,2,5,6)
d3 <- as.dendrogram(hclust(dist(x)))
labels(d3) <- x[order.dendrogram(d3)]
plot(d3)
Here is how we would do it for a more complex data object (where we may not want to play with the row names of the object, but to update the dendrogram):
if (!require(dendextend)) install.packages(dendextend);
library(dendextend)
x <- CO2[,4:5]
d4 <- as.dendrogram(hclust(dist(x)))
labels(d4) <- apply(CO2[,1:3], 1, paste, collapse = "_")[order.dendrogram(d4)]
d4 <- set(d4, "labels_cex", 0.6)
d4 <- color_branches(d4, k = 3)
par(mar = c(3,0,0,6))
plot(d4, horiz = T)
