R/ggEdgesBetweenAttributes.R

In krumsieklab/MoDentify: Phenotype-driven module identification

#' Plotting of the edges between attribute types
#'
#'
#' @param graph an \code{\link[igraph]{igraph}} object
#' @param name the name of the attribute
#' @param rm.unknown remove unknowns
#' @import ggplot2
#' @export
#' @import data.table
#' @import igraph
#' @importFrom stats setNames
#' @examples
#' data(qmdiab.data)
#' data(qmdiab.annos)
#' 
#' net.graph <- generateNetwork(data = qmdiab.data, annotations = qmdiab.annos)
#' ggEdgesBetweenAttributes(net.graph, "Super.pathway")
ggEdgesBetweenAttributes <- function(graph, name, rm.unknown = FALSE) {
  l <- lapply(E(graph), function(x)
    vertex_attr(graph = graph, name = name, index = as.vector(ends(graph = graph, es = x))))

  DT <- as.data.table(setNames(do.call(rbind.data.frame, l), c("att1", "att2")))

  if (rm.unknown) {
    DT <- DT[!grepl("Unknown", DT$att1), ]
    DT <- DT[!grepl("Unknown", DT$att2), ]
  }

  DT[, att1 := as.character(att1)]
  DT[, att2 := as.character(att2)]
  DT <- rbind(DT, DT[att1 != att2, .(att1 = att2, att2 = att1)])
  p <- ggplot(DT, aes(att1, att2)) + geom_bin2d() + theme(axis.text.x = element_text(angle = 90, hjust = 1))
  dat <- ggplot_build(p)$data[[1]]
  p + geom_text(data = dat, aes((xmin + xmax) / 2, (ymin + ymax) / 2, label = count), col = "white", size = 3) + ylab(name) + xlab(name)
}