[R] indexing into and modifying dendrograms

[Adaikalavan Ramasamy]

Probably not answering your questions here, but have you considered the
functions prune.tree and snip.tree from package tree or prune.rpart and
snip.rpart from the package rpart ?



On Mon, 2005-07-11 at 11:48 -0700, Jenny Bryan wrote:
> I would like to be able to exert certain types of control over the
> plotting of dendrograms (representing hierarchical clusterings) that I
> think is best achieved by modifying the dendrogram object
> prior to plotting.  I am using the "dendrogram" class and associated
> methods.
> 
> Define the cluster number of each cluster formed as the corresponding
> row of the merge object.  So, if you are clustering m objects, the
> cluster numbers range from 1 to m-1, with cluster m-1 containing all m
> objects, by definition.  I basically want a way to index into an
> object of class dendrogram using the above definition of cluster
> number and/or to act on a dendrogram, where I specify the target node
> using cluster number.
> 
> The first application would be to 'flip' the two elements in target
> node of the dendrogram (made clear in the small example below). (The
> setting is genomics and I have applications where I want to man-handle
> my dendrograms to make certain features of the clustering more obvious
> to the naked eye.)  I could imagine other, related actions that would
> be useful in decorating dendrograms.
> 
> I think I need a function that takes a dendrogram and cluster
> number(s) as input and returns the relevant part(s) of the dendrogram
> object -- but in a form that makes it easy to then, say, set certain
> attributes (perhaps recursively) for the target nodes (and perhaps
> those contained in it).  I'm including a small example below that
> hopefully illustrates this (it looks long, but it's mostly comments!).
> 
> Any help would be appreciated.
> 
> Jenny Bryan
> 
> ## get ready for step-by-step figures
> par(mfrow = c(2,2))
> 
> ## get 5 objects, with 2-dimensional features
> pts <- rbind(c(2,1.6),
>               c(1.8,2.4),
>               c(2.1, 2.7),
>               c(5,2.6),
>               c(4.7,3.1))
> plot(pts, xlim = c(0,6), ylim = c(0,4),type = "n",
>       xlab = "Feature 1", ylab = "Feature 2")
> points(pts,pch = as.character(1:5))
> 
> ## build a hierarhical tree, store as a dendrogram
> aggTree <- hclust(dist(pts), method = "single")
> (dend1 <- JB.as.dendrogram.hclust(aggTree))
> ## NOTE: only thing I added to official version of
> ## as.dendrogram.hclust:
> ## each node has an attribute cNum, which gives
> ## the merge step at which it was formed,
> ## i.e. gives the row of the merge object which
> ## describes the formation of that node
> ## one new line near end of nMerge loop:
> ## ***************
> ## *** 51,56 ****
> ## --- 51,60 ----
> ##   				     attr(z[[x[2]]], "midpoint"))/2
> ##   	}
> ##  	 attr(zk, "height") <- oHgt[k]
> ## +
> ## +         ## JB added July 6 2005
> ## +         attr(zk, "cNum") <- k
> ## +
> ##   	z[[k <- as.character(k)]] <- zk
> ##       }
> ##       z <- z[[k]]
> attributes(dend1)
> attributes(dend1[[1]])
> ## here's a table relating dend1 and the cNum attribute
> ## dend1               cNum
> ## -------------------------
> ## dend1                4
> ## dend1[[1]]           2
> ## dend1[[2]]           3
> ## dend1[[2]][[1]]  <not set>
> ## dend1[[2]][[1]]      1
> 
> ## use cNum attribute in "edgetext"
> ## following example in dendrogram documentation
> ## would really rather associate with the node than the edge
> ## but current plotting function has no notion of nodetext
> addE <- function(n) {
>    if(!is.leaf(n)) {
>      attr(n, "edgePar") <- list(p.col="plum")
>      attr(n, "edgetext") <- attr(n,"cNum")
>    }
>    n
> }
> dend2 <- dendrapply(dend1, addE)
> ## overlays the cNum ("cluster number") attribute on dendrogram
> plot(dend2, main = "dend2")
> ## why does no plum polygon appear around the '4' for the root
> ## edge?
> 
> ## swap order of clusters 2 and 3,
> ## i.e. 'flip' cluster 4
> dend3 <- dend2
> dend3[[1]] <- dend2[[2]]
> dend3[[2]] <- dend2[[1]]
> plot(dend3, main = "dend3")
> ## wish I could achieve with 'dend3 <- flip(dend2, cNum = 4)
> 
> ## swap order of cluster 1 and object 1,
> ## i.e. 'flip' cluster 3
> dend4 <- dend2
> dend4[[2]][[1]] <- dend2[[2]][[2]]
> dend4[[2]][[2]] <- dend2[[2]][[1]]
> plot(dend4, main = "dend4")
> ## wish I could achieve with 'dend4 <- flip(dend2, cNum = 3)
> 
> ## finally, it's clear that the midpoint attribute would also
> ## need to be modified by 'flip'
> 
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