R/vis_graph.R

In ceRNAnetsim: Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

#' Provides visualisation of the graph.
#'
#' `vis_graph` Provides visualisation of the graph.
#'
#' @importFrom ggraph ggraph geom_edge_link geom_node_point
#' create_layout theme_graph
#' @importFrom ggplot2 scale_colour_manual ggtitle
#' @importFrom igraph V 'V<-'
#' @return The graph object.
#'
#' @details vis_graph ensures the process to be followed.
#'
#' @param input_graph The graph object.
#' @param Competing_color The color of competing elements
#' on the graph with 'green' default.
#' @param mirna_color The color of miRNAs on the graph with
#' 'orange' default.
#' @param Upregulation The color of Upregulated elements on
#' the graph with 'red' default.
#' @param Downregulation The color of Downregulated elements
#' on the graph with 'blue' default.
#' @param title Title of the given graph.
#' @param layout The layout that will be used for
#' visualisation of the graph.
#'
#' @examples
#'
#' data('minsamp')
#' data('new_counts')
#'
#' # Visualisation of graph in steady-state.
#'
#'  priming_graph(minsamp, Competing_expression, miRNA_expression,
#'     aff_factor = c(seed_type,energy), deg_factor = region)%>%
#'    vis_graph()
#'
#' # Visualisation of graph after the change.
#'
#'  priming_graph(minsamp, Competing_expression, miRNA_expression,
#'     aff_factor = c(seed_type,energy), deg_factor = region)%>%
#'    update_variables(new_counts)%>%
#'    vis_graph()
#'
#' @export

vis_graph <- function(input_graph, Competing_color = "green", mirna_color = "orange",
                      Upregulation = "red", Downregulation = "blue", title = "GRAPH", layout = "kk") {

  if (missing(layout)) {
    warning("Kamada-Kawai (kk) layout was used.")
  }

  input_graph%>% ggraph(layout = layout) + 
                  geom_edge_link(colour = "#838B8B", alpha = 0.5) + 
                  geom_node_point(aes(filter = (changes_variable == "Competing"), color = "Competing", size = count_current), shape = 16) +
                  geom_node_point(aes(filter = (changes_variable == "miRNA"), color = "miRNA"),shape = 16, size = 2) + 
                  geom_node_point(aes(filter = (changes_variable =="Up"), color = "Up", size = count_current), shape = 16) + 
                  geom_node_point(aes(filter = (changes_variable == "Down"), color = "Down", size = count_current), shape = 16) + 
                  scale_colour_manual(name = "Types", values = c(Competing = Competing_color, miRNA = mirna_color, Up = Upregulation, Down = Downregulation)) + 
                  ggtitle(title) + theme_graph(base_family = "sans")


}