R/render_kinased_graph.R

In AliSajid/KINNET: Kinase INteraction NETwork Generation

#' Generate a 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
#'
#' @examples
#' TRUE
render_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()

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


    gr <-
      Rgraphviz::layoutGraph(network_graph, attrs = list(graph = list(rankdir = "TB")))
    graph::graphRenderInfo(gr)$fontsize <- 24
    graph::nodeRenderInfo(gr)$label <- mapped_kinases
    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)
    }

    invisible(gr)
  }