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\docType{methods}
\name{connectivity}
\alias{connectivity}
\alias{connectivity,ANY-method}
\alias{connectivity,factor-method}
\alias{connectivity-methods}
\alias{connectivity,NMF-method}
\alias{connectivity,numeric-method}
\alias{consensus}
\alias{consensus-methods}
\alias{consensus,NMFfitX-method}
\alias{consensus,NMF-method}
\title{Clustering Connectivity and Consensus Matrices}
\usage{
connectivity(object, ...)
\S4method{connectivity}{NMF}(object, no.attrib = FALSE)
consensus(object, ...)
}
\arguments{
\item{object}{an object with a suitable
\code{\link{predict}} method.}
\item{...}{extra arguments to allow extension. They are
passed to \code{\link{predict}}, except for the
\code{vector} and \code{factor} methods.}
\item{no.attrib}{a logical that indicates if attributes
containing information about the NMF model should be
attached to the result (\code{TRUE}) or not
(\code{FALSE}).}
}
\value{
a square matrix of dimension the number of samples in the
model, full of 0s or 1s.
}
\description{
\code{connectivity} is an S4 generic that computes the
connectivity matrix based on the clustering of samples
obtained from a model's \code{\link{predict}} method.
The consensus matrix has been proposed by \cite{Brunet et
al. (2004)} to help visualising and measuring the
stability of the clusters obtained by NMF approaches. For
objects of class \code{NMF} (e.g. results of a single NMF
run, or NMF models), the consensus matrix reduces to the
connectivity matrix.
}
\details{
The connectivity matrix of a given partition of a set of
samples (e.g. given as a cluster membership index) is the
matrix \eqn{C} containing only 0 or 1 entries such that:
\deqn{C_{ij} = \left\{\begin{array}{l} 1\mbox{ if sample
}i\mbox{ belongs to the same cluster as sample }j\\
0\mbox{ otherwise} \end{array}\right..}{ C_{ij} = 1 if
sample i belongs to the same cluster as sample j, 0
otherwise}
}
\section{Methods}{
\describe{
\item{connectivity}{\code{signature(object = "ANY")}:
Default method which computes the connectivity matrix
using the result of \code{predict(x, ...)} as cluster
membership index. }
\item{connectivity}{\code{signature(object = "factor")}:
Computes the connectivity matrix using \code{x} as
cluster membership index. }
\item{connectivity}{\code{signature(object = "numeric")}:
Equivalent to \code{connectivity(as.factor(x))}. }
\item{connectivity}{\code{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
\code{\link{predict,NMF-method}}. }
\item{consensus}{\code{signature(object = "NMFfitX")}:
Pure virtual method defined to ensure \code{consensus} is
defined for sub-classes of \code{NMFfitX}. It throws an
error if called. }
\item{consensus}{\code{signature(object = "NMF")}: This
method is provided for completeness and is identical to
\code{\link{connectivity}}, and returns the connectivity
matrix, which, in the case of a single NMF model, is also
the consensus matrix. }
\item{consensus}{\code{signature(object = "NMFfitX1")}:
The result is the matrix stored in slot
\sQuote{consensus}. This method returns \code{NULL} if
the consensus matrix is empty.
See \code{\link{consensus,NMFfitX1-method}} for more
details. }
\item{consensus}{\code{signature(object = "NMFfitXn")}:
This method returns \code{NULL} on an empty object. The
result is a matrix with several attributes attached, that
are used by plotting functions such as
\code{\link{consensusmap}} to annotate the plots.
See \code{\link{consensus,NMFfitXn-method}} for more
details. }
}
}
\examples{
\dontshow{# roxygen generated flag
options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
}
#----------
# connectivity,ANY-method
#----------
# clustering of random data
h <- hclust(dist(rmatrix(10,20)))
connectivity(cutree(h, 2))
#----------
# connectivity,factor-method
#----------
connectivity(gl(2, 4))
}
\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.
4164-9. ISSN 0027-8424, <URL:
http://dx.doi.org/10.1073/pnas.0308531101>, <URL:
http://www.ncbi.nlm.nih.gov/pubmed/15016911>.
}
\seealso{
\code{\link{predict}}
}
\keyword{methods}
|
