デンドログラム解析

目的†

デンドログラムのデータから、すべてのノードについて、ノードの情報（下にあるすべての リーフの数、高さ）を集めたい。

dendrapplyでは、返されるデータ構造が目的に沿っていなかった。

関数†

dend2nodelist <- function(hc) {
	n <- length(hc$labels)
	denMat <- matrix(rep(0,n*(n-1)),ncol <- (n-1))
	nodeData <- c()
	for(i in 1:(n-1)){
		j <- hc$merge[i,1]
		k <- hc$merge[i,2]
		if(j < 0){
			denMat[i,-j] <- 1
		}else{
			denMat[i, which(denMat[j,] == 1)] <- 1
		}
		if(k < 0){
			denMat[i,-k] <- 1
		}else{
			denMat[i, which(denMat[k,] == 1)] <- 1
		}
		leafs <- hc$labels[which(denMat[i,] == 1)]#リーフの一覧
		size <- length(leafs)#リーフの数
		nodeData <- rbind(
		nodeData,
		list(
			leafs = leafs,
			size = size,
			height = hc$height[i]
		))
	}
	nodeData
}

使い方†

> hc <- hclust(dist(USArrests[1:10,]))
> dend2nodelist(hc)
      leafs        size height  
 [1,] Character,2  2    16.80625
 [2,] Character,2  2    23.19418
 [3,] Character,2  2    25.09303
 [4,] Character,3  3    36.73486
 [5,] Character,3  3    45.18296
 [6,] Character,3  3    60.98073
 [7,] Character,6  6    77.19741
 [8,] Character,9  9    148.7357
 [9,] Character,10 10   226.303 
> dend2nodelist(hc)[1,]
$leafs
[1] "Alabama"  "Delaware"

$size
[1] 2

$height
[1] 16.80625

再帰的な書き方1†

f<-function(X){
  ret<-NULL
  f<-function(x){
    if(is.leaf(x)){
      attr(x,"label")
    }else{
      r<-c(sapply(x,f),recursive=T)
      ret<<-rbind(ret,list(leafs=r,size=attr(x,"members"),height=attr(x,"height")))
      r
    }
  }
  f(X)
  ret
}
r<-f(as.dendrogram(hclust(dist(USArrests), "ave")))

再帰的な書き方2†

dend2nodelist <- function(hc) {
	GetElement <- function(i, j) {
		if (i < 0) {
			if (j < 0) return(c(hc$labels[-i], hc$labels[-j]))
			else return(c(hc$labels[-i], GetElement(hc$merge[j,1], hc$merge[j,2])))
		} else {
			if (j < 0) return(c(GetElement(hc$merge[i,1], hc$merge[i,2]), hc$labels[-j]))
			else return(c(GetElement(hc$merge[i,1], hc$merge[i,2]), GetElement(hc$merge[j,1], hc$merge[j,2])))
		}
	}
	n <- length(hc$height)
	leafs <- NULL
	size <- integer(n)
	for (i in 1:n) {
		labels <- GetElement(hc$merge[i,1], hc$merge[i,2])
		size[i] <- length(labels)
		leafs[i] <- list(labels)
	}
	return(cbind(leafs=leafs, size=size, height=hc$height))
}

再帰的な書き方3†

dend2nodelist <- function(hc) {
 	temp <- function(hc, j) GetElement(hc$merge[j,1], hc$merge[j,2])
 	temp2 <- function(hc, j) if (j < 0) hc$labels[-j] else temp(hc, j)
 	GetElement <- function(i, j) if (i < 0) c(hc$labels[-i], temp2(hc, j)) 
                                    else c(temp(hc,i), temp2(hc, j))
 	leafs <- size <- integer(n <- length(hc$height))
 	for (i in 1:n) {size[i] <- length(labels <- temp(hc, i)); leafs[i] <- list(labels) }
 	return(cbind(leafs=leafs, size=size, height=hc$height))
}

実行例†

> hc <- hclust(dist(USArrests[1:10,]))
> result <- dend2nodelist(hc)

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