protoclust (version 1.6.4)

plotwithtext: Plot Dendrogram with Interior Node Text Added

Description

Makes a plot of the dendrogram (using plot.hclust) and adds interior node text.

Usage

plotwithtext(
  hc,
  imerge = -seq(n),
  text = as.character(1:n),
  bgcol = "white",
  font = 1,
  col = 1,
  cex = 1,
  ...
)

Arguments

hc

an object of class hclust

imerge

a vector of the nodes where text is desired. Interior nodes are numbered from 1 (lowest merge) to n - 1 (highest merge, i.e. the root) and leaf-nodes are negative. Example: seq(1, n - 1) means every interior node is labeled with text. Default: -seq(n), meaning all leaf labels and no interior-node labels are shown.

text

a character vector of length matching `imerge`. The element `text[i]` will label node `imerge[i]`.

bgcol

background color for labels

col, font

color and font of labels

cex

size of label

...

additional arguments to be passed to plot.hclust, such as hang

Details

This function lets one put text on a dendrogram. The argument imerge controls which interior nodes and leaves are labeled with text.

References

Bien, J., and Tibshirani, R. (2011), "Hierarchical Clustering with Prototypes via Minimax Linkage," The Journal of the American Statistical Association, 106(495), 1075-1084.

Examples

# NOT RUN {
# generate some data:
set.seed(1)
n <- 100
p <- 2
x <- matrix(rnorm(n * p), n, p)
rownames(x) <- paste("A", 1:n, sep="")
d <- dist(x)

# perform minimax linkage clustering:
hc <- protoclust(d)

# cut the tree to yield a 10-cluster clustering:
k <- 10 # number of clusters
cut <- protocut(hc, k=k)
h <- hc$height[n - k]

# plot dendrogram (and show cut):
protoclust:::plotwithtext(hc, imerge=cut$imerge, text=paste("Cluster", 1:k))
abline(h=h, lty=2)

# negative values of imerge specify which leaves to label
protoclust:::plotwithtext(hc, imerge=c(-1, cut$imerge), text=c("1", paste("Cluster", 1:k)))
# }