Rust-based ForceAtlas2 on a pre-computed graph — forceatlas2_from

Lays out any undirected graph with ForceAtlas2, for example an SNN graph or a graph from another package. Edge weights come from the weight edge attribute; without one, every edge weighs 1. Self-loops are dropped. Only the optimisation parameters in fa2_params are used; the graph and initialisation ones do not apply here.

Usage

forceatlas2_from_graph(
  graph,
  init = NULL,
  fa2_params = params_fa2(),
  seed = 42L,
  use_high_precision = NULL,
  .verbose = TRUE
)

Arguments

graph: An undirected igraph object without multi-edges. Use igraph::as_undirected(mode = "collapse") or igraph::simplify() to get there. If present, the weight edge attribute needs to be finite and non-negative.
init: Optional numerical matrix of dimensions vcount(graph) x 2. The initial layout, e.g. a UMAP of the same samples. If NULL, a random layout is used. Defaults to NULL.
fa2_params: Named list. ForceAtlas2 parameters, see params_fa2().
seed: Integer. Random seed for reproducibility. Defaults to 42L.
use_high_precision: Optional boolean. Gives fine-grained control over fp32 vs fp64 usage.
.verbose: Logical. Controls verbosity. Defaults to TRUE.

Value

A numerical matrix with dimensions vcount(graph) x 2 containing the ForceAtlas2 layout, rows in vertex order.

References

Jacomy, et al., PLoS ONE, 2014