order_nodes {speakeasyR}

Group nodes by community

Description

Reorders the graph to group nodes in the same community together. Useful for viewing community structure of a graph using a heatmap().

Usage

order_nodes(graph, membership, is_directed = "detect")

Arguments

graph

The graph or adjacency matrix the membership vector was created for.

membership

A vector or matrix listing node communities. The output from cluster() (should also work for other clustering algorithms that return membership in the same format).

is_directed

Whether the graph should be treated as directed or not. By default, if the graph is symmetric it is treated as undirected.

Details

Communities are ordered by size, so nodes in the largest community are first. Within a community, nodes are order by highest-to-lowest degree.

If membership is in matrix form (the output from cluster() with subcluster > 1) a matrix is returned with the indices for level one in row 1 and level n in row n. Each row reorders the communities of the previous row such that, at the second level, nodes are still grouped by the first level communities. This allows the hierarchical structure to be viewed.

See vignette for a multilevel example.

Value

An index vector or matrix. The number of rows are equal to the value of subcluster passed to cluster().

Examples

if (require("igraph")) {
  n_nodes <- 100
  n_types <- 3
  # Mixing parameter (likelihood an edge is between communities).
  mu <- 0.3
  pref <- matrix(mu, n_types, n_types)
  diag(pref) <- 1 - mu
  g <- igraph::preference.game(n_nodes, types = n_types, pref.matrix = pref)
  # Use a dense matrix representation to easily apply index.
  adj <- as(g[], "matrix")
  memb <- speakeasyR::cluster(adj, seed = 222, max_threads = 2)
  ordering <- speakeasyR::order_nodes(adj, memb)
  
  heatmap(adj[ordering, ordering], scale = "none", Rowv = NA, Colv = NA)
  
}