R/plot.network.R

In massiveGST: Competitive Gene Sets Test with the Mann-Whitney-Wilcoxon Test

plot.network <-
function(ttable, gs, eps = 0.25, similarity_threshold = 1/3, 
                         manipulation = FALSE, autoResize = TRUE, use.clustering = FALSE, 
                         edges.color = "#9E9E9E", ...) {
  if(use.clustering & !("clustering" %in% colnames(ttable))) {
    message("Error: no clustering found.")
    return(NULL)
  }
  similarity_matrix <- as.matrix(geneSets.sim(gs[rownames(ttable)], eps = eps))
  colnames(similarity_matrix) <- rownames(similarity_matrix) <- rownames(ttable)
  diag(similarity_matrix) <- 1
  similarity_matrix_tmp <- as.dist(similarity_matrix)
  similarity_matrix <- similarity_matrix > similarity_threshold
###
  min_node_size <- 10
  ttable$size.tmp <- sapply(ttable$actualSize, function(x) max(min_node_size, x))
  ttable$size.tmp <- floor(sapply(ttable$size.tmp, function(x) min_node_size+50*(2*(pnorm(x, sd = 250) -0.5))))
  ttable$color <- 1 + round(99 * pnorm(ttable$logit2NES, sd = 0.3))
  ttable$color <- colorRampPalette(c("green2", "red"))(100)[ttable$color]
########################################
  if(use.clustering) ttable$color <- ttable$clustering
#################################################
  nodes <- data.frame(id = 1:nrow(ttable), label = rownames(ttable), size = ttable$size.tmp, color = ttable$color)
###
  K <- nrow(ttable)
  edges <- data.frame(from = rep(2:K, (K-1):1), to = rep(1:(K-1), (K-1):1))
  for(k in 2:K) edges[which(edges[, "to"] == k-1), "from"] <- k:K
  wwhich <- which(unclass(as.dist(similarity_matrix)) > 0)
  edges <- edges[wwhich,]
  edges$color <- edges.color
  similarity_matrix_tmp <- similarity_matrix_tmp[wwhich]
  similarity_matrix_tmp <- (similarity_matrix_tmp - min(similarity_matrix_tmp))/(max(similarity_matrix_tmp) - min(similarity_matrix_tmp))
  similarity_matrix_tmp <- cut(similarity_matrix_tmp, include.lowest = TRUE, breaks = 0:10/10)
  edges$width <- as.numeric(similarity_matrix_tmp)
###
ans <- visNetwork(nodes, edges, ...)%>% 
  visOptions(manipulation = manipulation, autoResize = autoResize) %>%
  visIgraphLayout() 
return(ans)
}