complete_forceatlas2: Performs a Complete cycle of ForceAtlas2

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

Description

This function performs a complete (i.e. possibly including overlap resolution) cycle of the ForceAtlas2 force-directed layout algorithm

Usage

complete_forceatlas2(
  G,
  first.iter = 1000,
  overlap.method = NULL,
  overlap.iter = NULL,
  ...
)

Arguments

G	The input graph
first.iter	The maximum number of iterations in the first step, which is performed without overlap resolution
overlap.method	If this is NULL overlap resolution is not performed. Otherwise this should be a string specifying the overlap resolution method. Two options are possible "repel": This is the method used in the original ForceAtlas2 implementation. Using this method, a repulsive force is applied to nodes that overlap each other. This method can cause problem in cases where the layout is extremely crowded, as this repulsive force becomes the major determinant of the layout, and the nodes end up being arranged essentially in a grid "expand": In this method, the graph is linearly expanded, until no two nodes overlap anymore
overlap.iter	The maximum number of iterations for the overlap resolution step. This is only used if overlap.method is not NULL

Value

Returns an igraph object with two additional vertex attributes x and y, containing the x and y coordinates of the vertices in the final layout

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