Makes a plot of the dendrogram (using plot.hclust) and adds labels of
prototypes on the interior nodes of a dendrogram.
plotwithprototypes(
hc,
imerge = -seq(n),
labels = NULL,
bgcol = "white",
font = 1,
col = 1,
cex = 1,
...
)an object of class protoclust (as returned by the function
protoclust)
a vector of the nodes whose prototype labels should be added.
Interior nodes are numbered from 1 (lowest merge) to n - 1 (highest merge,
i.e. the root) and leaf-nodes are negative (so if element i is a prototype
for a singleton cluster, then -i is included in imerge). Example:
seq(1, n - 1) means every interior node is labeled with a prototype.
For larger trees, showing only the prototypes at a given cut may be easier
(described more below). Default: -seq(n), meaning all leaf labels and
no interior-node labels are shown.
an optional character vector of length n giving the labels of
the elements clustered. If not provided, hc$labels is used (if not NULL) or
else labels are taken to be seq(n).
background color for prototype labels
color and font of prototype labels
size of prototype label
additional arguments to be passed to plot.hclust, such as
hang
This function lets one put prototype labels on a dendrogram. The argument
imerge controls which interior nodes and leaves are labeled. A
convenient choice for the argument imerge is the imerge-output
of protocut. This allows one to label a dendrogram with the
prototypes of a particular cut. See examples below. This function is
called when one writes plot(hc), where hc is an object of
class protoclust.
Bien, J., and Tibshirani, R. (2011), "Hierarchical Clustering with Prototypes via Minimax Linkage," The Journal of the American Statistical Association, 106(495), 1075-1084.
# NOT RUN {
# generate some data:
set.seed(1)
n <- 100
p <- 2
x <- matrix(rnorm(n * p), n, p)
rownames(x) <- paste("A", 1:n, sep="")
d <- dist(x)
# perform minimax linkage clustering:
hc <- protoclust(d)
# cut the tree to yield a 10-cluster clustering:
k <- 10 # number of clusters
cut <- protocut(hc, k=k)
h <- hc$height[n - k]
# plot dendrogram (and show cut):
plotwithprototypes(hc, imerge=cut$imerge)
# or more simply: plot(hc, imerge=cut$imerge)
abline(h=h, lty=2)
# negative values of imerge specify which leaves to label
k2 <- 20 # more clusters... with two singletons
cut2 <- protocut(hc, k=k2)
h2 <- hc$height[n - k2]
plot(hc, hang=-1, imerge=cut2$imerge)
abline(h=h2, lty=2)
# }
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