R: Cut Out Clustering Level from Cluster Hierarchy

cutree-methods {apcluster} | R Documentation

## Cut Out Clustering Level from Cluster Hierarchy

### Description

Cut out a clustering level from a cluster hierarchy

### Usage

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

### 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.

### Value

returns an object of class `ExClust`

### Author(s)

Ulrich Bodenhofer & Andreas Kothmeier apcluster@bioinf.jku.at

### 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

    ## 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)

[Package apcluster version 1.4.7 Index]