DrL-class {dimRed} R Documentation

## Distributed Recursive Graph Layout

### Description

An S4 Class implementing Distributed recursive Graph Layout.

### Details

DrL uses a complex algorithm to avoid local minima in the graph embedding which uses several steps.

### 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

DrL can take the following 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_drl. The parameters maxiter, epsilon and kkconst are set to the default values and cannot be set, this may change in a future release. The DimRed Package adds an extra sparsity parameter by constructing a knn graph which also may improve visualization quality.

### References

Martin, S., Brown, W.M., Wylie, B.N., 2007. Dr.l: Distributed Recursive (graph) Layout (No. dRl; 002182MLTPL00). Sandia National Laboratories.

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

### Examples

## Not run:
if(requireNamespace(c("igraph", "coRanking"), quietly = TRUE)) {

dat <- loadDataSet("Swiss Roll", n = 200)
emb <- embed(dat, "DrL")
plot(emb, type = "2vars")
}

## End(Not run)



[Package dimRed version 0.2.6 Index]