Rotate leaf labels in pvclust dendrogram plot - r

Question

I'm using the pvclust package in R to perform bootstrapped hierarchical clustering. The output is then plotted as a hclust object with a few extra features (different default title, p-values at nodes). I've attached a link to one of the plots here.
This plot is exactly what I want, except that I need the leaf labels to be displayed horizontally instead of vertically. As far as I can tell there isn't an option for rotating the leaf labels in plot.hclust. I can plot the hclust object as a dendrogram
(i.e. plot(as.dendrogram(example$hclust), leaflab="textlike") instead of plot(example))
but the leaf labels are then printed in boxes that I can't seem to remove, and the heights of the nodes in the hclust object are lost. I've attached a link to the dendrogram plot here.
What would be the best way to make a plot that is as similar as possible to the standard plot.pvclust() output, but with horizontal leaf labels?

Answer 1

One way to get the text the way you want is to have plot.dendrogram print nothing and just add the labels yourself. Since you don't provide your data, I illustrate with some built-in data. By default, the plot was not leaving enough room for the labels, so I set the ylim to allow the extra needed room.
set.seed(1234)
HC = hclust(dist(iris[sample(150,6),1:4]))
plot(as.dendrogram(HC), leaflab="none", ylim=c(-0.2, max(HC$height)))
text(x=seq_along(HC$labels), y=-0.2, labels=HC$labels)

Answer 2

I've written a function that plots the standard pvclust plot with empty strings as leaf labels, then plots the leaf labels separately.
plot.pvclust2 <- function(clust, x_adj_val, y_adj_val, ...){
# Assign the labels in the hclust object to x_labels,
# then replace x$hclust$labels with empty strings.
# The pvclust object will be plotted as usual, but without
# any leaf labels.
clust_labels <- clust$hclust$labels
clust$hclust$labels <- rep("", length(clust_labels))
clust_merge <- clust$hclust$merge #For shorter commands
# Create empty vector for the y_heights and populate with height vals
y_heights <- numeric(length = length(clust_labels))
for(i in 1:nrow(clust_merge)){
# For i-th merge
singletons <- clust_merge[i,] < 0 #negative entries in merge indicate
#agglomerations of singletons, and
#positive entries indicate agglomerations
#of non-singletons.
y_index <- - clust_merge[i, singletons]
y_heights[y_index] <- clust$hclust$height[i] - y_adj_val
}
# Horizontal text can be cutoff by the margins, so the x_adjust moves values
# on the left of a cluster to the right, and values on the right of a cluster
# are moved to the left
x_adjust <- numeric(length = length(clust_labels))
# Values in column 1 of clust_merge are on the left of a cluster, column 2
# holds the right-hand values
x_adjust[-clust_merge[clust_merge[ ,1] < 0, 1]] <- 1 * x_adj_val
x_adjust[-clust_merge[clust_merge[ ,2] < 0, 2]] <- -1 * x_adj_val
# Plot the pvclust object with empty labels, then plot horizontal labels
plot(clust, ...)
text(x = seq(1, length(clust_labels)) +
x_adjust[clust$hclust$order],
y = y_heights[clust$hclust$order],
labels = clust_labels[clust$hclust$order])
}