| 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 |
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 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
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)