Rust-based ForceAtlas2 — forceatlas2 • manifoldsR

Lays out the kNN graph of the data with ForceAtlas2, the way scanpy's draw_graph does: the kNN graph is turned into the UMAP fuzzy union graph and every edge pulls, every node pair pushes (1/d, with masses 1 + degree), plus gravity towards the origin. Repulsion runs on a Barnes-Hut tree. Already have a graph? Use forceatlas2_from_graph().

Usage

forceatlas2(
  data,
  knn = NULL,
  k = 15L,
  knn_method = c("kmknn", "balltree", "hnsw", "annoy", "nndescent", "exhaustive", "ivf"),
  nn_params = params_nn(),
  fa2_params = params_fa2(),
  seed = 42L,
  use_high_precision = NULL,
  .verbose = TRUE
)

Arguments

data: Numerical matrix or data frame. The data to embed of shape samples x features. Will be coerced to a matrix.
knn: Optional NearestNeighbours class. If provided, the k-nearest neighbour search is skipped and this one is used. Defaults to NULL.
k: Integer. Number of nearest neighbours. Defaults to 15L.
knn_method: Character. (Approximate) Nearest neighbour method to use. One of "kmknn", "hnsw", "annoy", "nndescent", "balltree", "ivf" or "exhaustive". Defaults to "kmknn".
nn_params: Named list. Nearest neighbour search parameters, see params_nn().
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 samples x 2 containing the ForceAtlas2 layout.

References

Jacomy, et al., PLoS ONE, 2014