layout_umap: UMAP graph layouts

layout_umapR Documentation

UMAP graph layouts

Description

Using the UMAP dimensionality reduction algorithm as a graph layout

Usage

layout_with_umap(g, pivots = NULL, ...)

layout_igraph_umap(g, circular, ...)

Arguments

g

igraph object

pivots

if not NULL, number of pivot nodes to use for distance calculation (for large graphs).

...

additional parameters for umap. See the ?uwot::umap for help.

circular

not used

Details

The layout_igraph_* function should not be used directly. It is only used as an argument for plotting with 'igraph'. UMAP can be tuned by many different parameters. Refer to the documentation at https://github.com/jlmelville/uwot for help

Value

matrix of xy coordinates

Author(s)

David Schoch

References

McInnes, Leland, John Healy, and James Melville. "Umap: Uniform manifold approximation and projection for dimension reduction." arXiv preprint arXiv:1802.03426 (2018).

Examples

library(igraph)

g <- sample_islands(10,20,0.6,10)
xy <- layout_with_umap(g,min_dist = 0.5)

graphlayouts documentation built on Nov. 24, 2022, 9:07 a.m.