minor

R/plotfunctions.R

 #'Visualizes RNAMagnet output as a signaling network
 #'
 #'@param rnamagnet An object of class \code{\link{rnamagnet}}, as produced by \code{\link{RNAMagnetSignaling}}
-#'@param return Determines object to return; one of "summary" or "rnamagnet-class"
+#'@param score One of \code{specificity} or \code{volume}, see detail below.
 #'@param threshold Threshold interaction strength for including an edge in the network.
 #'@param colors A named vector of colors to be used for plotting; names correspond to levels of \code{rnamagnet@class}
 #'@param useLabels Plot the population labels on the graph?
 #'@param ... Parameters passed to \code{\link[igraph]{plot.igraph}}, e.g. a layout can be stored as described in the example code below
+#'@details If \code{score} is set to \code{specificity}, two cell types are connected if they are enriched for interactions.
+#'@details If \code{score} is set to \code{volume}, two cell types are connected if there are many interactions between them.
+#'@details To understand the difference, consider the following example of three cell types A, B, and C, where A expresses 50 different cytokines to which both B and C express cognate receptors. B expresses 10 cytokines, for which only C expresses cognate receptors. If plotting the number of interactions, A would be connected to B and C; if plotting their specificity, B would be connected to C.
 #'@examples
 #'\dontrun{
 #'network <- PlotSignalingNetwork(rnamagnet_result)
@@ -14,20 +17,31 @@
 #'}
 #'@return Plots the network and invisibly returns an object of class \code{\link[igraph]{igraph}}
 #'@export
-PlotSignalingNetwork <- function(rnamagnet, threshold = 0.01, colors = NULL, useLabels=T, ...) {
+PlotSignalingNetwork <- function(rnamagnet, score = "specificity", threshold = ifelse(score == "specificity", 0.01,10), colors = NULL, useLabels=T, ...) {
 
   pops <- colnames(rnamagnet@specificity)
+
+  if (tolower(score) == "specificity"){
   mean_by_pop <- sapply(pops, function(id) {
     sapply(pops, function(id2) {
       mean(rnamagnet@specificity[rnamagnet@celltype == id2,id])
     })
   })
+  factor <- 1000
+  } else if (tolower(score) == "volume"){
+    mean_by_pop <- sapply(pops, function(id) {
+      sapply(pops, function(id2) {
+        mean(rnamagnet@interaction[rnamagnet@celltype == id2,id])
+      })
+    })
+    factor <- 0.1
+  } else stop("Score must be set to one of specificity or volume")
 
   graphf <- reshape2::melt(t(mean_by_pop))
 
   colnames(graphf) <- c("sender", "receiver", "value")
   graphf$sender <- as.character(graphf$sender); graphf$receiver <- as.character(graphf$receiver);
-  graphf$width <- graphf$value^1.5 *1000
+  graphf$width <- graphf$value^1.5 *factor
 
   vertices <- data.frame(id = unique(graphf$sender), size = 5, stringsAsFactors = F, label = unique(graphf$sender))