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 |
|
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 and Andreas Kothmeier
References
https://github.com/UBod/apcluster
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
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))