apcluster (version 1.4.7)

cutree-methods: Cut Out Clustering Level from Cluster Hierarchy

Description

Cut out a clustering level from a cluster hierarchy

Usage

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

Arguments

tree

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

k

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

h

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

Value

returns an object of class '>ExClust

Details

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.

References

http://www.bioinf.jku.at/software/apcluster

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

See Also

'>AggExResult, '>ExClust

Examples

# NOT RUN {
## 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
show(aggres)

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

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