R: Fruchterman Reingold Graph Layout

FruchtermanReingold-class {dimRed} | R Documentation

## Fruchterman Reingold Graph Layout

### Description

An S4 Class implementing the Fruchterman Reingold Graph Layout algorithm.

### 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

ndim

  The number of dimensions, defaults to 2. Can only be 2 or 3

knn

  Reduce the graph to keep only the neares neighbors. Defaults to 100.

d

  The distance function to determine the weights of the graph edges. Defaults to euclidean distances.

### Implementation

Wraps around `layout_with_fr`, see there for details. The Fruchterman Reingold algorithm puts the data into a circle and puts connected points close to each other.

### References

Fruchterman, T.M.J., Reingold, E.M., 1991. Graph drawing by force-directed placement. Softw: Pract. Exper. 21, 1129-1164. https://doi.org/10.1002/spe.4380211102

### See Also

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

### Examples

    dat <- loadDataSet("Swiss Roll", n = 100)

    ## use the S4 Class directly:
    fruchterman_reingold <- FruchtermanReingold()
    pars <- fruchterman_reingold@stdpars
    pars$knn <- 5
    emb <- fruchterman_reingold@fun(dat, pars)

    ## simpler, use embed():
    emb2 <- embed(dat, "FruchtermanReingold", knn = 5)

    plot(emb, type = "2vars")

[Package dimRed version 0.2.3 Index]