在pvclust树形图中旋转叶标签

Question

我正在使用R中的pvclust包来执行自举层次聚类。然后将输出绘制为具有一些额外特征的hclust对象（不同的默认标题，节点处的p值）。 I've attached a link to one of the plots here.

这个图正是我想要的，除了我需要水平显示叶标签而不是垂直显示。据我所知，没有选项可以在plot.hclust中旋转叶子标签。我可以将hclust对象绘制为树形图

（即plot(as.dendrogram(example$hclust), leaflab="textlike")代替plot(example)）

但是叶子标签然后打印在我似乎无法移除的框中，并且hclust对象中节点的高度将丢失。 I've attached a link to the dendrogram plot here.

制作与标准plot.pvclust()输出尽可能相似但使用水平叶标签的情节的最佳方法是什么？

Answer 1

以您想要的方式获取文本的一种方法是让plot.dendrogram不打印任何内容，只需自己添加标签即可。由于您不提供数据，我会使用一些内置数据进行说明。默认情况下，图表没有为标签留出足够的空间，因此我设置ylim以允许额外需要的空间。

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

我编写了一个函数，将带有空字符串的标准pvclust图绘制为叶标签，然后分别绘制叶标签。

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])
}