NMF: nneg – R documentation

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nneg

Transforming from Mixed-sign to Nonnegative Data

Description

nneg is a generic function to transform a data objects that contains negative values into a similar object that only contains values that are nonnegative or greater than a given threshold.

posneg is a shortcut for nneg(..., method='posneg'), to split mixed-sign data into its positive and negative part. See description for method "posneg", in nneg.

rposneg performs the "reverse" transformation of the posneg function.

Usage

nneg(object, ...)

  ## S4 method for signature 'matrix'
nneg(object,
    method = c("pmax", "posneg", "absolute", "min"),
    threshold = 0, shift = TRUE)

  posneg(...)

  rposneg(object, ...)

  ## S4 method for signature 'matrix'
rposneg(object, unstack = TRUE)

Arguments

`object`	The data object to transform
`...`	extra arguments to allow extension or passed down to `nneg,matrix` or `rposneg,matrix` in subsequent calls.
`method`	Name of the transformation method to use, that is partially matched against the following possible methods: pmax Each entry is constrained to be above threshold `threshold`. posneg The matrix is split into its "positive" and "negative" parts, with the entries of each part constrained to be above threshold `threshold`. The result consists in these two parts stacked in rows (i.e. `rbind`-ed) into a single matrix, which has double the number of rows of the input matrix `object`. absolute The absolute value of each entry is constrained to be above threshold `threshold`. min Global shift by adding the minimum entry to each entry, only if it is negative, and then apply threshold.
`threshold`	Nonnegative lower threshold value (single numeric). See argument `shit` for details on how the threshold is used and affects the result.
`shift`	a logical indicating whether the entries below the threshold value `threshold` should be forced (shifted) to 0 (default) or to the threshold value itself. In other words, if `shift=TRUE` (default) all entries in the result matrix are either 0 or strictly greater than `threshold`. They are all greater or equal than `threshold` otherwise.
`unstack`	Logical indicating whether the positive and negative parts should be unstacked and combined into a matrix as `pos - neg`, which contains half the number of rows of `object` (default), or left stacked as `[pos; -neg]`.

Value

an object of the same class as argument object.

an object of the same type of object

Methods

nneg: signature(object = "matrix"): Transforms a mixed-sign matrix into a nonnegative matrix, optionally apply a lower threshold. This is the workhorse method, that is eventually called by all other methods defined in the NMF package.
nneg: signature(object = "NMF"): Apply nneg to the basis matrix of an NMF object (i.e. basis(object)). All extra arguments in ... are passed to the method nneg,matrix.
rposneg: signature(object = "NMF"): Apply rposneg to the basis matrix of an NMF object.

Examples

#----------
# nneg,matrix-method
#----------
# random mixed sign data (normal distribution)
set.seed(1)
x <- rmatrix(5,5, rnorm, mean=0, sd=5)
x

# pmax (default)
nneg(x)
# using a threshold
nneg(x, threshold=2)
# without shifting the entries lower than threshold
nneg(x, threshold=2, shift=FALSE)

# posneg: split positive and negative part
nneg(x, method='posneg')
nneg(x, method='pos', threshold=2)

# absolute
nneg(x, method='absolute')
nneg(x, method='abs', threshold=2)

# min
nneg(x, method='min')
nneg(x, method='min', threshold=2)

#----------
# nneg,NMF-method
#----------
# random
M <- nmfModel(x, rmatrix(ncol(x), 3))
nnM <- nneg(M)
basis(nnM)
# mixture coefficients are not affected
identical( coef(M), coef(nnM) )

#----------
# posneg
#----------
# shortcut for the "posneg" transformation
posneg(x)
posneg(x, 2)

#----------
# rposneg,matrix-method
#----------
# random mixed sign data (normal distribution)
set.seed(1)
x <- rmatrix(5,5, rnorm, mean=0, sd=5)
x

# posneg-transform: split positive and negative part
y <- posneg(x)
dim(y)
# posneg-reverse
z <- rposneg(y)
identical(x, z)
rposneg(y, unstack=FALSE)

# But posneg-transformation with a non zero threshold is not reversible
y1 <- posneg(x, 1)
identical(rposneg(y1), x)

#----------
# rposneg,NMF-method
#----------
# random mixed signed NMF model
M <- nmfModel(rmatrix(10, 3, rnorm), rmatrix(3, 4))
# split positive and negative part
nnM <- posneg(M)
M2 <- rposneg(nnM)
identical(M, M2)

NMF

Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

v0.23.0

GPL (>= 2)

Authors

Renaud Gaujoux, Cathal Seoighe

Initial release

2020-07-30