R/graphLayout.R

In JoelleJee/DGOplot: DO and GO Enrichment Analyses Plotting

#' A simplified function from NetPathMiner by ahmohamed reconstructed
#' https://stackoverflow.com/questions/28715736/how-to-spread-out-community-graph-made-by-using-igraph-package-in-r/28722680#28722680
#'
#' A helper function with an algorithm to spread out the nodes in an association network. 
#' 
#' @param graph garph
#' @param wc number of vertices added for algorithm
#' @param cluster.strength cluster strength
#' @param layout layout
#'
#' @return Returns a layout for the gene association network
#' 
#' @import igraph

netLayout <- function(graph, wc, cluster.strength=10,layout=layout.auto) { 
  # create a lightweight copy of graph w/o the attributes.
  gCopy <- igraph::graph.edgelist(igraph::get.edgelist(graph)) 
  E(gCopy)$weight <- 1
  
  attr <- cbind(id=1:vcount(gCopy), val=wc)
  gCopy <- gCopy + igraph::vertices(unique(attr[,2])) + igraph::edges(unlist(t(attr)), 
                                      weight=cluster.strength)
  # coordinates of the nodes
  coords <- layout(gCopy, weights=E(gCopy)$weight)[1:igraph::vcount(graph),]
  
  return(coords)
}