R: Non-Negative Matrix Factorization

NNMF-class {dimRed} | R Documentation

## Non-Negative Matrix Factorization

### Description

S4 Class implementing NNMF.

### Details

NNMF is a method for decomposing a matrix into a smaller dimension such that the constraint that the data (and the projection) are not negative is taken into account.

### Slots

`fun`

  A function that does the embedding and returns a dimRedResult object.

`stdpars`

  The standard parameters for the function.

### General usage

Dimensionality reduction methods are S4 Classes that either be used directly, in which case they have to be initialized and a full list with parameters has to be handed to the `@fun()` slot, or the method name be passed to the embed function and parameters can be given to the `...`, in which case missing parameters will be replaced by the ones in the `@stdpars`.

### Parameters

The method can take the following parameters:

ndim

  The number of output dimensions.

method

  character, which algorithm should be used. See `nmf` for possible values. Defaults to "brunet"

nrun

  integer, the number of times the computations are conducted. See `nmf`

seed

  integer, a value to control the random numbers used.

options

  named list, other options to pass to `nmf`

### Implementation

Wraps around `nmf`. Note that the estimation uses random numbers. To create reproducible results, set the random number seed in the function call. Also, in many cases, the computations will be conducted in parallel using multiple cores. To disable this, use the option `.pbackend = NULL`.

### References

Lee, D.D., Seung, H.S., 1999. Learning the parts of objects by non-negative matrix factorization. Nature 401, 788-791. https://doi.org/10.1038/44565

### See Also

Other dimensionality reduction methods: `AutoEncoder-class`, `DRR-class`, `DiffusionMaps-class`, `DrL-class`, `FastICA-class`, `FruchtermanReingold-class`, `HLLE-class`, `Isomap-class`, `KamadaKawai-class`, `LLE-class`, `MDS-class`, `PCA-class`, `PCA_L1-class`, `UMAP-class`, `dimRedMethod-class`, `dimRedMethodList()`, `kPCA-class`, `nMDS-class`, `tSNE-class`

### Examples

    set.seed(4646)
    dat <- loadDataSet("Iris")
    emb <- embed(dat, "NNMF")

    plot(emb)

    # project new values:
    nn_proj <- predict(emb, dat[1:7])
    plot(nn_proj)

[Package dimRed version 0.2.4 Index]