layout_forceatlas2: ForceAtlas2 force-directed layout

In ParkerICI/scgraphs: Analyzing single-cell data using graphs

Description

ForceAtlas2 force-directed layout

Usage

layout_forceatlas2(
  G,
  ew.influence = 1,
  kgrav = 1,
  iter = 1000,
  prevent.overlap = FALSE,
  fixed = NULL,
  stopping.tolerance = 0.001,
  barnes.hut = FALSE
)

Arguments

G	The input igraph object. The graph must have an edge attribute named weight, representing edge weights
ew.influence	Edge weight influence. The edge weights are set to edge.weight ^ ew.influence before the calculation (see original ForceAtlas2 publication)
kgrav	The gravity constant. Higher values will result in more compact graphs (see original ForceAtlas2 publication)
iter	Maximum number of iterations. The algorithm will stop after this many iterations, or when the average displacement of the nodes between two iterations is less than the stopping.tolerance threshold (see below)
prevent.overlap	Set this option to TRUE to prevent the nodes from overlapping (see ForceAtlas2 description)
fixed	A boolean vector of length equal to the number of nodes in the graph which specifies which nodes, need to be held in a fixed position. If this is NULL (default), no nodes are held fixed
stopping.tolerance	The algorithm will stop after either iter number of iterations, or when the average displacement of the nodes between two iterations is less than this threshold
barnes.hut	Whether to use the Barnes-Hut approximation for speeding up the calculations when dealing with large graphs. This option is automatically set to true when the graph has more than 2000 nodes

Value

this function returns a list with three elements

• lay: a numeric matrix with two columns containing the x and y coordinates of each node in the final layout

• avg.displ: a numeric vector containing the average displacement of the vertices at each iteration

• max.displ: a numeric vector containing the maximum displacement between all the vertices after each iteration

References

http://gephi.github.io

Jacomy M1, Venturini T, Heymann S, Bastian M. ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the Gephi software. PLoS One. 2014 Jun 10;9(6):e98679. doi: 10.1371/journal.pone.0098679

ParkerICI/scgraphs documentation built on April 30, 2021, 1:10 p.m.