Skip to contents

Wrapper function to generate ForceAtlas2 parameters

params_fa2.Rd

The graph, initialisation and optimisation knobs for ForceAtlas2. local_connectivity, bandwidth, init and randomised only apply when the graph is built from the data via forceatlas2(); forceatlas2_from_graph() ignores them.

Usage

params_fa2(
  local_connectivity = 1,
  bandwidth = 1e-05,
  n_epochs = 500L,
  scaling_ratio = 2,
  gravity = 1,
  strong_gravity = FALSE,
  lin_log = FALSE,
  dissuade_hubs = FALSE,
  edge_weight_influence = 1,
  jitter_tolerance = 1,
  theta = 1.2,
  init = c("spectral", "pca", "random"),
  randomised = FALSE
)

Arguments

local_connectivity

Numeric. Number of nearest neighbours assumed to be at distance zero. Defaults to 1.0.

bandwidth

Numeric. Convergence tolerance for smooth kNN distance binary search. Defaults to 1e-05.

n_epochs

Integer. Number of optimisation epochs. Defaults to 500L.

scaling_ratio

Numeric. Repulsion strength. Larger values spread the layout. Defaults to 2.0.

gravity

Numeric. Pull towards the origin. Keeps disconnected components from drifting off. Defaults to 1.0.

strong_gravity

Boolean. Distance-independent gravity, scaled by scaling_ratio. Defaults to FALSE.

lin_log

Boolean. Logarithmic attraction (LinLog). Gives tighter communities. Defaults to FALSE.

dissuade_hubs

Boolean. Divide the attraction by the node mass. Pushes hubs to the periphery. Defaults to FALSE.

edge_weight_influence

Numeric. Exponent applied to the edge weights. 0 ignores the weights. Defaults to 1.0.

jitter_tolerance

Numeric. Tolerated swinging. Larger is faster but less precise. Defaults to 1.0.

theta

Numeric. Barnes-Hut opening parameter on Gephi's scale. 0 gives the exact repulsion. Defaults to 1.2.

init

String. Embedding initialisation method. One of c("spectral", "pca", "random"). Defaults to "spectral".

randomised

Boolean. Use randomised SVD for PCA initialisation. Defaults to FALSE.

Value

A named list with the following elements:

  • local_connectivity - Numeric. Number of nearest neighbours assumed to be at distance zero. Defaults to 1.0.

  • bandwidth - Numeric. Convergence tolerance for smooth kNN distance binary search. Defaults to 1e-05.

  • n_epochs - Integer. Number of optimisation epochs. Defaults to 500L.

  • scaling_ratio - Numeric. Repulsion strength. Larger values spread the layout. Defaults to 2.0.

  • gravity - Numeric. Pull towards the origin. Keeps disconnected components from drifting off. Defaults to 1.0.

  • strong_gravity - Boolean. Distance-independent gravity, scaled by scaling_ratio. Defaults to FALSE.

  • lin_log - Boolean. Logarithmic attraction (LinLog). Gives tighter communities. Defaults to FALSE.

  • dissuade_hubs - Boolean. Divide the attraction by the node mass. Pushes hubs to the periphery. Defaults to FALSE.

  • edge_weight_influence - Numeric. Exponent applied to the edge weights. 0 ignores the weights. Defaults to 1.0.

  • jitter_tolerance - Numeric. Tolerated swinging. Larger is faster but less precise. Defaults to 1.0.

  • theta - Numeric. Barnes-Hut opening parameter on Gephi's scale. 0 gives the exact repulsion. Defaults to 1.2.

  • init - String. Embedding initialisation method. One of c("spectral", "pca", "random"). Defaults to "spectral".

  • randomised - Boolean. Use randomised SVD for PCA initialisation. Defaults to FALSE.

References

Jacomy, et al., PLoS ONE, 2014