R/simulation_plot.R

In dcanr: Differential co-expression/association network analysis

#' @include statistical_tests.R
NULL

#' @title Plot source and true differential networks from simulations
#' @description Plots either the source network or the true differential network
#'   for all KDs performed in the simulation. KD nodes are coloured with their
#'   resulting differential networks coloured accordingly.
#'
#' @inheritParams getSimData
#' @param what a character, indicating which network to retrieve, 'source'
#'   (default), 'direct', 'influence' or 'association'
#' @param ... additional parameters to \code{plot.igraph}
#'
#' @details The direct, influence and association networks represent different
#'   levels of true differential networks. The direct network contains
#'   differential regulatory interactions present in the original network. The
#'   influence network includes upstream interactions and the association
#'   network includes non-causative differential interactions.
#'
#' @return a plot of the network
#'
#' @seealso \code{\link[igraph]{plot.igraph}}
#'
#' @examples
#' data(sim102)
#' plotSimNetwork(sim102)
#' plotSimNetwork(sim102, what = 'direct')
#' plotSimNetwork(sim102, what = 'influence')
#' plotSimNetwork(sim102, what = 'association')
#'
#' @export
plotSimNetwork <- function(simulation, what = c('source', 'direct', 'influence', 'association'), ...) {
  what = match.arg(what)
  if (what == 'source') {
    net = simulation$staticnet
  } else {
    what = stringr::str_to_title(what)
    infnet = simulation$infnet
    E(infnet)$color[!igraph::get.edge.attribute(infnet, what)] = NA
    net = infnet
  }

  #add layout
  V(net)$x = simulation$netlayout[, 1]
  V(net)$y = simulation$netlayout[, 2]

  igraph::plot.igraph(net, ...)
}