cutree-methods {apcluster}R Documentation

Cut Out Clustering Level from Cluster Hierarchy


Cut out a clustering level from a cluster hierarchy


## S4 method for signature 'AggExResult'
cutree(tree, k, h)
## S4 method for signature 'APResult'
cutree(tree, k, h)



an object of class AggExResult containing a cluster hierarchy; may also be an object of class APResult


the level (i.e. the number of clusters) to be selected


alternatively, the level can be selected by specifying a cut-off for the merging objective


The function cutree extracts a clustering level from a cluster hierarchy stored in an AggExResult object. Which level is selected can be determined by one of the two arguments k and h (see above). If both k and h are specified, k overrides h. This is done largely analogous to the standard function cutree. The differences are (1) that only one level can be extracted at a time and (2) that an ExClust is returned instead of an index list.

The function cutree may further be used to convert an APResult object into an ExClust object. In this case, the arguments k and h are ignored.


returns an object of class ExClust


Ulrich Bodenhofer & Andreas Kothmeier


Bodenhofer, U., Kothmeier, A., and Hochreiter, S. (2011) APCluster: an R package for affinity propagation clustering. Bioinformatics 27, 2463-2464. DOI: doi:10.1093/bioinformatics/btr406.

See Also

AggExResult, ExClust


## create two simple clusters
x <- c(1, 2, 3, 7, 8, 9)
names(x) <- c("a", "b", "c", "d", "e", "f")

## compute similarity matrix (negative squared distance)
sim <- negDistMat(x, r=2)

## run affinity propagation
aggres <- aggExCluster(sim)

## show details of clustering results

## retrieve clustering with 2 clusters
cutree(aggres, 2)

## retrieve clustering with cut-off h=-1
cutree(aggres, h=-1)

[Package apcluster version 1.4.11 Index]