R/network_pcxn.R

In hidelab/pcxn.db: Pathway correlation coefficients and p values between pre-defined gene sets

# FUNCTION
# - arguments: dataframe taken from explore or analyze functions
# - returns: correlation network with colored nodes and thick/thin edges

# NOTES
# - edge width has been adjust to represent absolute correlation x10 
# (the multiplication is done in order for the edges to 
# have visibly different width)
# - edge color is either blue (positive correlation) 
# or red (negative correlation). The amount of correlation is 
# represented by edge width

utils::globalVariables(c("igraph", "layout_in_circle","make_graph","V","V<-",
                         "tkplot"))

#' Create a network of a pcxn object
#'
#' @param df pcxn object created by explore or analyze functions
#'
#' @return tkplot object representing the network
#' @export
#'
#' @examples
#' \dontrun{
#' network <- network_pcxn(df)
#' }

network_pcxn <- function(df) {

  # requireNamespace(igraph)

  edges <- c()
  edge_thickness <- c()
  edge_color <- c()

  for (i in 1:nrow(df@data)) {
    edges <- c(edges, df@data[i,1])
    edges <- c(edges, df@data[i,2])
    edge_thickness <- c(edge_thickness, abs(as.numeric(df@data[i,3]) * 10))
    if(as.numeric(df@data[i,3]) < 0) edge_color <- c(edge_color, "blue")
    else edge_color <- c(edge_color, "red")
  }

  graph <- igraph::make_graph(edges, directed = FALSE)

  # setting node colours
  if (df@type == "explore") {
    V(graph)$color <- "#ffaf1a"
    V(graph)[df@geneset_groups$query_geneset]$color[1] <- "#66b2ff"
  }
  if (df@type == "analyze") {
    V(graph)$color <- "white"
    for(i in 1:length(df@geneset_groups$top_correlated_genesets)) {
      tryCatch({
        cgs <-  df@geneset_groups$top_correlated_genesets[i]
        V(graph)[cgs]$color <- "#ffaf1a"
      }, error = function(e) {
        print(paste("No edges containing ", cgs, 
                    " pass the correlation and p-value filters therefore the 
                    node is not included in the network",sep = ""))

      })
    }
    for(j in 1:length(df@geneset_groups$phenotype_0_genesets)) {
      tryCatch({
        cgs1 <-  df@geneset_groups$phenotype_0_genesets[j]
        V(graph)[cgs1]$color <- "#66b2ff"
      }, error = function(e) {
        print(paste("No edges containing ", cgs1, 
                    " pass the correlation and p-value filters therefore the 
                    node is not included in the network",sep = ""))
      })
    }
    for(h in 1:length(df@geneset_groups$phenotype_1_genesets)) {
      tryCatch({
        cgs2 <-  df@geneset_groups$phenotype_1_genesets[h]
        V(graph)[cgs2]$color <- "#19c67e"
      }, error = function(e) {
        print(paste("No edges containing ", cgs2, 
                    " pass the correlation and p-value filters therefore the 
                    node is not included in the network",sep = ""))
      })
    }
  }

  # drawing the plot
  plot <- igraph::tkplot(graph, layout= igraph::layout_in_circle, width = NULL, height = NULL,
                 edge.width = edge_thickness, edge.color = edge_color)

  return(plot)
}