合并多个hclust对象(或树状图)

Question

是否有一种简单的方法可以在根处合并多个hclust对象(或树状图)？

为了说明我的问题，我把这个例子做得尽可能完整。

假设我想按区域对USArrests进行聚类，然后将所有的hclust对象联合起来，在一个热图中将它们绘制在一起。

USArrests
Northeast <- c("Connecticut", "Maine", "Massachusetts", "New Hampshire", "Rhode Island", 
"Vermont", "New Jersey", "New York", "Pennsylvania")
Midwest <-  c("Illinois", "Indiana", "Michigan", "Ohio",  "Wisconsin", 
    "Iowa", "Kansas", "Minnesota", "Missouri", "Nebraska", "North Dakota", 
    "South Dakota")
South <- c("Delaware", "Florida", "Georgia", "Maryland", "North Carolina", 
           "South Carolina", "Virginia", "West Virginia", 
           "Alabama", "Kentucky", "Mississippi", "Tennessee", "Arkansas", 
           "Louisiana", "Oklahoma", "Texas")
West <- c("Arizona", "Colorado", "Idaho", "Montana", "Nevada", "New Mexico", 
          "Utah", "Wyoming", "Alaska", "California", "Hawaii", "Oregon", "Washington")

h1 <- hclust(dist(USArrests[Northeast,]))
h2 <- hclust(dist(USArrests[Midwest,]))
h3 <- hclust(dist(USArrests[South,]))
h4 <- hclust(dist(USArrests[West,]))

现在我有了4个hclust对象(h1通过h4)。我通常是这样合并的：

hc <- as.hclust(merge(merge(merge(
    as.dendrogram(h1), as.dendrogram(h2)), as.dendrogram(h3)), 
    as.dendrogram(h4)))

然后，要绘制它们，我必须根据hclust对象重新排序矩阵，然后再绘制(我添加了一些注释以使绘图更清晰)：

usarr <- USArrests[c(Northeast, Midwest, South, West),]

region_annotation <- data.frame(Region = c(rep("Northeast", length(Northeast)), 
                                rep("Midwest", length(Midwest)),
                                rep("South", length(South)),
                                rep("West", length(West))),
                                row.names = c(Northeast, Midwest, South, West))

pheatmap(usarr, cluster_rows = hc, 
         annotation_row = region_annotation)

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总之:有比合并所有单独的集群更容易做到这一点的方法吗？

Answer 1

最后，我做了几个函数来更自动地完成这个任务。(在我的版本中，我还增加了对相关性“距离”的支持，因此它要大一点)

hclust_semisupervised <- function(data, groups, dist_method = "euclidean",
                                  dist_p = 2, hclust_method = "complete") {
    hclist <- lapply(groups, function (group) {
        hclust(dist(data[group,], method = dist_method, p = dist_p), method = hclust_method)
    })
    hc <- .merge_hclust(hclist)
    data_reordered <- data[unlist(groups),]

    return(list(data = data_reordered, hclust = hc))
}

.merge_hclust <- function(hclist) {
    #-- Merge
    d <- as.dendrogram(hclist[[1]])
    for (i in 2:length(hclist)) {
        d <- merge(d, as.dendrogram(hclist[[i]]))
    }
    as.hclust(d)
}

有了USArrests和区域向量，我就这样调用hclust_semisupervised：

semi_hc <- hclust_semisupervised(USArrests, list(Northeast, Midwest, South, West)

现在绘制热图：

pheatmap(semi_hc$data, cluster_rows = semi_hc$hclust, 
         annotation_row = region_annotation)

Answer 2

要创建合并的hclust对象，可以在使用new.env创建的自定义环境中安全地使用new.env。

在不使用<<-的情况下，可能有其他方法一次创建两个合并的对象。希望有人能点亮它。

我试着使用do.call('merge', list( dendrograms of h1, h2, h3, h4 )。但是它没有工作，因为hclust需要在顶部有两个分支，而不是4个分支。

代码：

library('pheatmap')
myenv <- new.env()
myenv$hc <- as.dendrogram( hclust( dist(USArrests[Northeast,])))
invisible( lapply( list( Midwest, South, West), function(x){
  myenv$hc <<- merge( myenv$hc, as.dendrogram( hclust( dist( USArrests[ x, ]) )) )
  NULL
} ) )
myenv$hc <- as.hclust(myenv$hc)

图：

pheatmap(usarr, cluster_rows = myenv$hc, 
         annotation_row = region_annotation)

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