# Plot Dendrogram with Prototype Labels Added Makes a plot of the dendrogram (using `plot.hclust`) and adds labels of prototypes on the interior nodes of a dendrogram. ```r plotwithprototypes( hc, imerge = -seq(n), labels = NULL, bgcol = "white", font = 1, col = 1, cex = 1, ... ) ``` ## Arguments - `hc`: an object of class `protoclust` (as returned by the function `protoclust`) - `imerge`: 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. - `labels`: an optional character vector of length n giving the labels of the elements clustered. If not provided, hc$labels is used (if not NULL) or else labels are taken to be `seq(n)`. - `bgcol`: background color for prototype labels - `col, font`: color and font of prototype labels - `cex`: size of prototype label - `...`: additional arguments to be passed to `plot.hclust`, such as `hang` ## Details This function lets one put prototype labels on a dendrogram. The argument `imerge` controls which interior nodes and leaves are labeled. A convenient choice for the argument `imerge` is the `imerge`-output of `protocut`. This allows one to label a dendrogram with the prototypes of a particular cut. See examples below. This function is called when one writes `plot(hc)`, where `hc` is an object of class `protoclust`. ## Examples ```r # generate some data: set.seed(1) n <- 100 p <- 2 x <- matrix(rnorm(n * p), n, p) rownames(x) <- paste("A", 1:n, sep="") d <- dist(x) # perform minimax linkage clustering: hc <- protoclust(d) # cut the tree to yield a 10-cluster clustering: k <- 10 # number of clusters cut <- protocut(hc, k=k) h <- hc$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) ``` ## 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. ## See Also `protoclust`, `protocut` ## Author(s) Jacob Bien and Rob Tibshirani

plotwithprototypes function