R/render_reduced_kinased_graph.R

In CogDisResLab/KINNET: Kinase INteraction NETwork Generation

#' Generate a reduced kianse graph
#'
#' @param analysis_result Object output from assign_kinases()
#' @param title Title of the graph
#' @param render logical. Whether a graph should be rendered or not.
#'
#' @return a graph object
#' @export
#'
#' @import bnlearn dplyr
#' @importFrom rlang .data
#' @importFrom graph graphRenderInfo nodeRenderInfo edgeRenderInfo
#' @importFrom Rgraphviz layoutGraph renderGraph
#' @importFrom tibble as_tibble
#'
#' @examples
#' TRUE
render_reduced_kinased_graph <-
  function(analysis_result, title, render = FALSE) {
    mapped_kinases <- analysis_result$mapped_kinases %>%
      dplyr::select(.data$peptide, .data$kinase) %>%
      dplyr::group_by(.data$peptide) %>%
      dplyr::slice_head(n = 1) %>%
      tibble::deframe()

    net_arcs <- bnlearn::arcs(analysis_result$net)

    mapped_net_arcs <- net_arcs %>%
      tibble::as_tibble() %>%
      mutate(from = mapped_kinases[.data$from],
             to = mapped_kinases[.data$to]) %>%
      unique() %>%
      dplyr::filter(.data$from != .data$to) %>%
      as.matrix()

    bn <- bnlearn::empty.graph(unique(c(mapped_net_arcs)))
    bnlearn::arcs(bn, check.cycles = FALSE, check.illegal = FALSE) <-
      mapped_net_arcs

    network_graph <- bnlearn::graphviz.plot(bn,
                                            shape = "ellipse",
                                            layout = "fdp",
                                            main = title)


    gr <-
      Rgraphviz::layoutGraph(network_graph, attrs = list(graph = list(rankdir = "TB")))
    graph::graphRenderInfo(gr)$fontsize <- 24
    graph::nodeRenderInfo(gr)$fontsize <- 14
    graph::nodeRenderInfo(gr)$fixedsize <- TRUE
    graph::nodeRenderInfo(gr)$height <- 25
    graph::nodeRenderInfo(gr)$lWidth <- 37.5
    graph::nodeRenderInfo(gr)$rWidth <- 37.5
    graph::edgeRenderInfo(gr)$weight <- 20

    if (render == TRUE) {
      Rgraphviz::renderGraph(gr)
    }

    out <- list(bnnet = bn,
                graphviz_plot = gr)

    invisible(out)
  }