simplify_igraph_network: Simplify an igraph network such that consecutive linear edges...

In dynwrap: Representing and Inferring Single-Cell Trajectories

Simplify an igraph network such that consecutive linear edges are removed

Description

• Nodes with degree 2 (or indegree 1 and outdegree 1) are removed: A -> B -> C becomes A -> C

• Cycles contain at least 3 nodes, ie. A -> B -> A becomes A -> B -> C -> A

• Loops are converted to a cycle, unless allow_self_loops = TRUE

• Duplicated edges are removed, unless allow_duplcated_edges = FALSE

Usage

simplify_igraph_network(
  gr,
  allow_duplicated_edges = TRUE,
  allow_self_loops = TRUE,
  force_keep = NULL,
  edge_points = NULL
)

Arguments

gr	An igraph object, see igraph::graph()
allow_duplicated_edges	Whether or not to allow duplicated edges between nodes.
allow_self_loops	Whether or not to allow self loops.
force_keep	Nodes that will not be removed under any condition
edge_points	Points that are on edges

Value

An igraph object, or a list with an igraph object and a data frame with edge points

Examples

net <- data.frame(
  from = 1:2,
  to = 2:3,
  length = 1,
  directed = TRUE,
  stringsAsFactors = F
)
gr <- igraph::graph_from_data_frame(net)
simplify_igraph_network(gr)

net <- data.frame(
  from = c(1, 2, 3, 1),
   to = c(2, 3, 1, 4),
    length = 1,
    directed = TRUE,
    stringsAsFactors = F
)
gr <- igraph::graph_from_data_frame(net)
simplify_igraph_network(gr)

net <- data.frame(
  from = c(1, 2, 3, 4),
   to = c(2, 3, 1, 5),
    length = 1,
    directed = TRUE,
    stringsAsFactors = F
)
gr <- igraph::graph_from_data_frame(net)
simplify_igraph_network(gr)

dynwrap documentation built on July 26, 2023, 5:15 p.m.