R/graph.R

In travisbyrum/constructnet: Network reconstruction from time series

#' Utilities for creating and interacting with graph objects.
#'
#' @param A input MATRIX
#'
#' @param mode Character scalar, specifies how igraph should interpret the supplied matrix.
#' @param remove_self_loops If True, remove the diagonal of the matrix before creating the
#'                          graph object.
#'
#' @export
create_graph <- function(A, mode = NULL, remove_self_loops = T) {
  if (remove_self_loops) {
    diag(A) <- 0
  }
  
  if (is.null(mode)) {
    if (suppressWarnings(all(A == t(A), tolerance = (1e-05 * abs(t(A)) + 1e-08)))) {
      G <- igraph::graph_from_adjacency_matrix(A, mode = "undirected")
      G <- igraph::simplify(G, remove.multiple = T, remove.loops = T)
    } else {
      G <- igraph::graph_from_adjacency_matrix(A, mode = "directed")
      G <- igraph::simplify(G, remove.multiple = T, remove.loops = T)
    }
  } else {
    G <- igraph::graph_from_adjacency_matrix(A, mode = mode)
    G <- igraph::simplify(G, remove.multiple = T, remove.loops = T)
  }
  
  G
}