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
,
MDS-class
,
NNMF-class
,
PCA-class
,
PCA_L1-class
,
UMAP-class
,
dimRedMethod-class
,
dimRedMethodList()
,
kPCA-class
,
nMDS-class
,
tSNE-class
Examples
if(requireNamespace(c("igraph", "coRanking"), quietly = TRUE)) {
dat <- loadDataSet("Swiss Roll", n = 100)
emb <- embed(dat, "FruchtermanReingold")
plot(emb, type = "2vars")
}