layout_umap function

UMAP graph layouts

Using the UMAP dimensionality reduction algorithm as a graph layout

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

Returns

matrix of xy coordinates

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

Examples

library(igraph)

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

References

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

Author(s)

David Schoch