R: Generate label vector from clustering result

labels-methods {apcluster} | R Documentation

## Generate label vector from clustering result

### Description

Generate a label vector from an clustering result

### Usage

    ## S4 method for signature 'ExClust'
    labels(object, type="names")

### Arguments

`object` | object of class `APResult` or `ExClust`
`type` | specifies which kind of label vector should be created, see details below

### Details

The function `labels` creates a label vector from a clustering result. Which kind of labels are produced is controlled by the argument `type`:

“names”

  (default) returns the name of the exemplar to which each data sample belongs to; if no names are available, the function stops with an error;

“enum”

  returns the index of the cluster to which each data sample belongs to, where clusters are enumerated consecutively from 1 to the number of clusters (analogous to other clustering methods like `kmeans`);

“exemplars”

  returns the index of the exemplar to which each data sample belongs to, where indices of exemplars are within the original data, which is nothing else but the slot `object@idx` with attributes removed.

### Value

returns a label vector as long as the number of samples in the original data set

### 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

`APResult`, `ExClust`, `cutree`

### 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
    apres <- apcluster(sim)

    ## show details of clustering results
    show(apres)

    ## label vector (names of exemplars)
    labels(apres)

    ## label vector (consecutive index of exemplars)
    labels(apres, type="enum")

    ## label vector (index of exemplars within original data set)
    labels(apres, type="exemplars")

    ## now with agglomerative clustering
    aggres <- aggExCluster(sim)

    ## label (names of exemplars)
    labels(cutree(aggres, 2))

[Package apcluster version 1.4.7 Index]