connectivity  R Documentation 
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.
connectivity(object, ...) ## S4 method for signature 'NMF' connectivity(object, no.attrib = FALSE) consensus(object, ...)
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 ( 
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
a square matrix of dimension the number of samples in the model, full of 0s or 1s.
signature(object = "ANY")
:
Default method which computes the connectivity matrix
using the result of predict(x, ...)
as cluster
membership index.
signature(object = "factor")
:
Computes the connectivity matrix using x
as
cluster membership index.
signature(object = "numeric")
:
Equivalent to connectivity(as.factor(x))
.
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. See
predict,NMFmethod
.
signature(object = "NMFfitX")
:
Pure virtual method defined to ensure consensus
is
defined for subclasses of NMFfitX
. It throws an
error if called.
signature(object = "NMF")
: This
method is provided for completeness and is identical to
connectivity
, and returns the connectivity
matrix, which, in the case of a single NMF model, is also
the consensus matrix.
signature(object = "NMFfitX1")
:
The result is the matrix stored in slot
‘consensus’. This method returns NULL
if
the consensus matrix is empty.
See consensus,NMFfitX1method
for more
details.
signature(object = "NMFfitXn")
:
This method returns NULL
on an empty object. The
result is a matrix with several attributes attached, that
are used by plotting functions such as
consensusmap
to annotate the plots.
See consensus,NMFfitXnmethod
for more
details.
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>.
predict
# # connectivity,ANYmethod # # clustering of random data h < hclust(dist(rmatrix(10,20))) connectivity(cutree(h, 2)) # # connectivity,factormethod # connectivity(gl(2, 4))
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