sort_average: Sorting and reordering dendrogram nodes by average distances

In dendsort: Modular Leaf Ordering Methods for Dendrogram Nodes

Description

sort_average sorts a dendrogram object based on the average distance of its subtrees, recursively. 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

sort_average(d)

Arguments

d	A dendrogram object.d

Value

output A sorted dendrogram object.

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.