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#' Sorting and reordering dendrogram nodes
#'
#' \code{dendsort} sorts a dendrogram object which is
#' typically a result of hierarchical clustering (hclust). The
#' subtrees in the resulting dendrogram are sorted based on the
#' average distance of subtrees at every merging point. The
#' tighter cluster, in other words the cluster with smaller
#' average distance, is placed on the left side of branch.
#' When a leaf merge with a cluster, the leaf is placed on the
#' right side.
#'
#' @param d a dendrogram or hclust object.\code{d}
#' @param isReverse logical indicating if the order should be reversed.Defaults to FALSE\code{isReverse}
#' @param type character indicating the type of sorting. Default to "min" \code{type}
#' @return output A sorted dendrogram or hclust.
#' @keywords dendrogram
#' @export dendsort
#' @aliases dendsort
#'
#' @examples
#' #generate sample data
#' set.seed(1234); par(mar=c(0,0,0,0))
#' x <- rnorm(10, mean=rep(1:5, each=2), sd=0.4)
#' y <- rnorm(10, mean=rep(c(1,2), each=5), sd=0.4)
#' dataFrame <- data.frame(x=x, y=y, row.names=c(1:10))
#' #calculate Euclidian distance
#' distxy <- dist(dataFrame)
#' #hierachical clustering "complete" linkage by default
#' hc <- hclust(distxy)
#'
#' #sort dendrogram
#' dd <- dendsort(as.dendrogram(hc))
#' hc_sorted <- as.hclust(dd)
#'
#' #sort in reverse, you can also pass hclust object
#' plot(dendsort(hc, isReverse=TRUE))
#'
#' #sort by average distance
#' plot(dendsort(hc, type="average"))
#'
#' #plot the result
#' par(mfrow = c(1, 3), mai=c(0.8,0.8,2,0.8))
#' plot(x, y, col="gray", pch=19, cex=2)
#' text(x, y, labels=as.character(1:10), cex=0.9)
#' plot(hc,main="before sorting", xlab="", sub="")
#' plot(hc_sorted, main="after sorting", xlab="", sub="")
#'
dendsort <- function(d, isReverse=FALSE, type="min") {
if(!inherits(d, "dendrogram") && !inherits(d, "hclust")){
stop("d variable must be a dendrogram or hclust object")
}
#assign dendrogram
dend = d
if(inherits(d, "hclust")){
dend = as.dendrogram(d)
}
#type string to lower case
type = tolower(type)
if(type=="average"){
#sort by average distance
if(isReverse){
#sort in reverse
n = sort_average_r(dend)
}else{
#sort in left to right order
n = sort_average(dend)
}
}else if(type == "min"){
#sort by smallest distance
if(isReverse){
n = sort_smallest_r(dend)
}else{
n = sort_smallest(dend)
}
}else{
stop("unrecognized type variable "+type)
}
#if input was a hclust object, convert it back to hclust
if(inherits(d, "hclust")){
n = as.hclust(n)
}
return(n)
}
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