Clustering Connectivity and Consensus Matrices
Description
connectivity
is an S4 generic that computes the
connectivity matrix based on the clustering of samples
obtained from a model's predict
method.
The consensus matrix has been proposed by Brunet et
al. (2004) to help visualising and measuring the
stability of the clusters obtained by NMF approaches. For
objects of class NMF
(e.g. results of a single NMF
run, or NMF models), the consensus matrix reduces to the
connectivity matrix.
Usage
1 2 3 4 5 6  connectivity(object, ...)
## S4 method for signature 'NMF'
connectivity(object, no.attrib = FALSE)
consensus(object, ...)

Arguments
object 
an object with a suitable

... 
extra arguments to allow extension. They are
passed to 
no.attrib 
a logical that indicates if attributes
containing information about the NMF model should be
attached to the result ( 
Details
The connectivity matrix of a given partition of a set of samples (e.g. given as a cluster membership index) is the matrix C containing only 0 or 1 entries such that:
C_{ij} = 1 if sample i belongs to the same cluster as sample j, 0 otherwise
Value
a square matrix of dimension the number of samples in the model, full of 0s or 1s.
Methods
 connectivity
signature(object = "ANY")
: Default method which computes the connectivity matrix using the result ofpredict(x, ...)
as cluster membership index. connectivity
signature(object = "factor")
: Computes the connectivity matrix usingx
as cluster membership index. connectivity
signature(object = "numeric")
: Equivalent toconnectivity(as.factor(x))
. connectivity
signature(object = "NMF")
: Computes the connectivity matrix for an NMF model, for which cluster membership is given by the most contributing basis component in each sample. Seepredict,NMFmethod
. consensus
signature(object = "NMFfitX")
: Pure virtual method defined to ensureconsensus
is defined for subclasses ofNMFfitX
. It throws an error if called. consensus
signature(object = "NMF")
: This method is provided for completeness and is identical toconnectivity
, and returns the connectivity matrix, which, in the case of a single NMF model, is also the consensus matrix. consensus
signature(object = "NMFfitX1")
: The result is the matrix stored in slot ‘consensus’. This method returnsNULL
if the consensus matrix is empty.See
consensus,NMFfitX1method
for more details. consensus
signature(object = "NMFfitXn")
: This method returnsNULL
on an empty object. The result is a matrix with several attributes attached, that are used by plotting functions such asconsensusmap
to annotate the plots.See
consensus,NMFfitXnmethod
for more details.
References
Brunet J, Tamayo P, Golub TR and Mesirov JP (2004). "Metagenes and molecular pattern discovery using matrix factorization." _Proceedings of the National Academy of Sciences of the United States of America_, *101*(12), pp. 41649. ISSN 00278424, <URL: http://dx.doi.org/10.1073/pnas.0308531101>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/15016911>.
See Also
predict
Examples
1 2 3 4 5 6 7 8 9 10 11  #
# connectivity,ANYmethod
#
# clustering of random data
h < hclust(dist(rmatrix(10,20)))
connectivity(cutree(h, 2))
#
# connectivity,factormethod
#
connectivity(gl(2, 4))
