R/visualizeNetwork.R

In ASpediaFI: ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

#' Network visualization
#'
#' This function visualizes a heterogeneous network pertaining to specific
#' pathway.
#'
#' @param pathway.id name of pathway
#' @param net an igraph object containing a heterogeneous network produced
#' by DRaWR.
#' @param n number of genes and AS events to show
#' @keywords internal
#' @return plot of a pathway-specific network
#' @import igraph
#' @importFrom graphics par
#' @importFrom limma strsplit2
#' @noRd
visualizeNetwork <- function(pathway.id, net, n = 10) {
    neighbor.genes <- neighbors(net, pathway.id, "all")
    neighbor.genes <-
        neighbor.genes$name[order(
            neighbor.genes$prob, decreasing = TRUE)]
    neighbor.genes <- neighbor.genes[seq_len(min(n, length(neighbor.genes)))]
    AS.vs <- V(net)[V(net)$type == "AS"]
    neighbor.AS <- unique(unlist(lapply(neighbor.genes, function(x) {
        tmp <- neighbors(net, x, "all")
        tmp <- tmp$name[tmp$type == "AS"]
        tmp
    })))
    neighbor.AS <- AS.vs[AS.vs$name %in% neighbor.AS]
    neighbor.AS <- neighbor.AS$name[order(neighbor.AS$prob,
                                            decreasing = TRUE)]
    neighbor.AS <- neighbor.AS[seq_len(min(n, length(neighbor.AS)))]
    subnet <- suppressWarnings(subgraph(net, c(neighbor.genes, neighbor.AS)))

    par(mar = c(0, 0, 0, 0))
    V(subnet)$label <- ifelse(V(subnet)$type == "gene",
                                V(subnet)$name,
                                apply(strsplit2(V(subnet)$name,
                                                    split = ":")[, seq_len(2)],
                                        1,
                                        function(x) paste(x, collapse = "\n")))
    V(subnet)$color <- ifelse(V(subnet)$type == "gene", "white", "lightblue")
    V(subnet)$shape <- ifelse(V(subnet)$type == "gene", "circle", "square")
    E(subnet)$lty <- ifelse(E(subnet)$type == "PPI", 1, 2)
    E(subnet)$weight <- 1

    plot(subnet, vertex.label.color = "black", vertex.size = 25,
            layout = layout_with_lgl(subnet, area = vcount(subnet)^3),
            edge.color = "black", edge.width = 2)
}