R/drawNetworkWithModules.R

In krumsieklab/MoDentify: Phenotype-driven module identification

#' Draw Network with Modules
#'
#'
#' @param graph an \code{\link[igraph]{igraph}} object, which can be generated by
#' \code{\link{generateNetwork}}.
#' @param title a name for the Cytoscape session.
#' @param nodes  \code{\link[data.table]{data.table}} with data containing the nodes.
#' It is contained in the output list of \code{\link{identifyModules}}.
#' @param colors a colour palette as returned from
#' \code{\link[grDevices]{rainbow}} for colouring the different modules.
#' @param save.image TRUE, if modules should be saved as png files.
#' @param close.cycnets.afterwards TRUE, if the windows in the cytoscape environment should be closed
#' after drawing. This might be useful repeated function call.
#'
#'
#' @import RCy3
#' @import data.table
#' @import igraph
#' @export
#' @usage drawNetworkWithModules(graph, title, nodes, colors, save.image=TRUE,
#' close.cycnets.afterwards = FALSE)
#' @references
#' \insertRef{Shannon2003}{MoDentify}
#' @references
#' \insertRef{Smoot2011}{MoDentify}
#' @references
#' \insertRef{RCy3}{MoDentify}
#'
drawNetworkWithModules <- function(graph, title, nodes, colors, save.image = TRUE,
                                   close.cycnets.afterwards = FALSE) {
  nodes <- nodes
  module_graph <- graph
  for (i in seq_len(dim(nodes)[1])) {
    if ("Fluid" %in% vertex_attr_names(graph)) {
      module_graph <- set_vertex_attr(
        module_graph, "Labels", nodes[i]$name,
        paste0(
          toupper(substr(vertex_attr(graph, "Fluid", nodes[i]$name), 0, 1)),
          "::", nodes[i]$label
        )
      )
    } else {
      module_graph <- set_vertex_attr(module_graph, "Labels", nodes[i]$name, nodes[i]$label)
    }

    module_graph <- set_vertex_attr(module_graph, "module.name", nodes[i]$name, nodes[i]$moduleID)
    module_graph <- set_vertex_attr(module_graph, "p.value", nodes[i]$name, nodes[i]$node.pval)
    module_graph <- set_vertex_attr(module_graph, "is.significant", nodes[i]$name, nodes[i]$is.significant)
  }

  netSUID <- createNetworkFromIgraph(igraph = module_graph, title = title)


  setNodeSizeMapping("p.value", c(0.05 / vcount(graph), 0.1), c(100, 75, 40, 25), default.size = c(20))
  setNodeShapeMapping("is.significant", c("TRUE", "FALSE"), c("diamond", "ellipse"))
  setNodeColorMapping("module.name", names(colors), c(substr(colors, 0, 7)), mapping.type = "d")
  layoutNetwork(layout.name = "kamada-kawai")

  if (save.image) {
    exportImage(
      filename = paste0(getwd(), "/", title, ".png"), type = "png",
      resolution = 600, height = 1600
    )
  }

  if (close.cycnets.afterwards) {
    closeSession()
  }
}