dendsort: Sorting and reordering dendrogram nodes

In dendsort: Modular Leaf Ordering Methods for Dendrogram Nodes

Description

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.

Usage

dendsort(d, isReverse = FALSE, type = "min")

Arguments

d	a dendrogram or hclust object.d
isReverse	logical indicating if the order should be reversed.Defaults to FALSEisReverse
type	character indicating the type of sorting. Default to "min" type

Value

output A sorted dendrogram or hclust.

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 documentation built on April 20, 2021, 5:05 p.m.