
Cut out a clustering level from a cluster hierarchy
# S4 method for AggExResult
cutree(tree, k, h)
# S4 method for APResult
cutree(tree, k, h)
returns an object of class ExClust
an object of class AggExResult
containing a cluster hierarchy; may also be an object of
class APResult
the level (i.e. the number of clusters) to be selected
alternatively, the level can be selected by specifying a cut-off for the merging objective
Ulrich Bodenhofer & Andreas Kothmeier apcluster@bioinf.jku.at
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.
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: tools:::Rd_expr_doi("10.1093/bioinformatics/btr406").
AggExResult
,
ExClust
## 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)
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