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rplotdendrogramhclustpvclust
JSneathThompson
JSneathThompson

Reputation: 53

Rotate leaf labels in pvclust dendrogram plot

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?

Upvotes: 0

Views: 1134

Answers (2)

JSneathThompson
JSneathThompson

Reputation: 53

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])
}

Upvotes: 0

G5W
G5W

Reputation: 37641

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)

Dendrogram with horizontal labels

Upvotes: 1

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