Dimension names for NMF objects
The methods dimnames, rownames,
colnames and basisnames and their
respective replacement form allow to get and set the
dimension names of the matrix factors in a NMF model.
dimnames returns all the dimension names in a
single list. Its replacement form dimnames<-
allows to set all dimension names at once.
rownames, colnames and basisnames
provide separate access to each of these dimension names
respectively. Their respective replacement form allow to
set each dimension names separately.
basisnames(x, ...) basisnames(x, ...)<-value ## S4 method for signature 'NMF' dimnames(x) ## S4 replacement method for signature 'NMF' dimnames(x)<-value
x |
an object with suitable |
... |
extra argument to allow extension. |
value |
a character vector, or |
The function basisnames is a new S4 generic
defined in the package NMF, that returns the names of the
basis components of an object. Its default method should
work for any object, that has a suitable basis
method defined for its class.
Overall, these methods behave as their equivalent on
matrix objects. The function basisnames<-
ensures that the dimension names are handled in a
consistent way on both factors, enforcing the names on
both matrix factors simultaneously.
The function basisnames<- is a new S4 generic
defined in the package NMF, that sets the names of the
basis components of an object. Its default method should
work for any object, that has suitable basis<- and
coef<- methods method defined for its class.
signature(x = "ANY"): Default
method which returns the column names of the basis matrix
extracted from x, using the basis method.
For NMF objects these also correspond to the row names of the coefficient matrix.
signature(x = "ANY"): Default
method which sets, respectively, the row and the column
names of the basis matrix and coefficient matrix of
x to value.
signature(x = "NMF"): Returns the
dimension names of the NMF model x.
It returns either NULL if no dimnames are set on the object, or a 3-length list containing the row names of the basis matrix, the column names of the mixture coefficient matrix, and the column names of the basis matrix (i.e. the names of the basis components).
signature(x = "NMF"): sets the
dimension names of the NMF model x.
value can be NULL which resets all
dimension names, or a 1, 2 or 3-length list providing
names at least for the rows of the basis matrix.
The optional second element of value (NULL if
absent) is used to set the column names of the
coefficient matrix. The optional third element of
value (NULL if absent) is used to set both the
column names of the basis matrix and the row names of the
coefficient matrix.
# create a random NMF object
a <- rnmf(2, 5, 3)
# set dimensions
dims <- list( features=paste('f', 1:nrow(a), sep='')
, samples=paste('s', 1:ncol(a), sep='')
, basis=paste('b', 1:nbasis(a), sep='') )
dimnames(a) <- dims
dimnames(a)
basis(a)
coef(a)
# access the dimensions separately
rownames(a)
colnames(a)
basisnames(a)
# set only the first dimension (rows of basis): the other two dimnames are set to NULL
dimnames(a) <- dims[1]
dimnames(a)
basis(a)
coef(a)
# set only the two first dimensions (rows and columns of basis and coef respectively):
# the basisnames are set to NULL
dimnames(a) <- dims[1:2]
dimnames(a)
basis(a)
# reset the dimensions
dimnames(a) <- NULL
dimnames(a)
basis(a)
coef(a)
# set each dimensions separately
rownames(a) <- paste('X', 1:nrow(a), sep='') # only affect rows of basis
basis(a)
colnames(a) <- paste('Y', 1:ncol(a), sep='') # only affect columns of coef
coef(a)
basisnames(a) <- paste('Z', 1:nbasis(a), sep='') # affect both basis and coef matrices
basis(a)
coef(a)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.