Fixing plot.mcGP

R/plotGraph.R

@@ -5,38 +5,38 @@
 #' have coordinates, additionally a scatterplot of the nodes in the euclidean
 #' plane is generated.
 #'
-#' @template arg_mcGP
 #' @param show.cluster.centers [\code{logical(1)}]\cr
 #'   Display cluster centers?
 #'   Default is \code{TRUE}. This option is ignored silently if the instance is not clustered.
 #' @param ... [any]\cr
 #'   Not used at the moment.
-#' @param x Not used at the moment.
+#' @param x [\code{mcGP}]\cr
+#'   Multi-objective graph problem.
 #' @param y Not used at the moment.
 #' @return [\code{list}] A list of \code{\link[ggplot2]{ggplot}} objects with components
 #' \code{pl.weights} (scatterplot of edge weights) and eventually \code{pl.coords} (scatterplot of
 #' nodes). The latter is \code{NULL}, if \code{graph} has no associated coordinates.
 #' @export
-plot.mcGP = function(graph, show.cluster.centers = TRUE, x=NULL, y=NULL, ...) {  
+plot.mcGP = function(x, y=NULL, show.cluster.centers = TRUE, ...) {  
 
   assertFlag(show.cluster.centers)
 
   pl.coords = NULL
-  n.nodes = graph$n.nodes
-  n.clusters = graph$n.clusters
-  n.weights = graph$n.weights
+  n.nodes = x$n.nodes
+  n.clusters = x$n.clusters
+  n.weights = x$n.weights
   if (n.weights > 2L)
     stopf("plot.mcGP: More than 2 weights are currently not supported.")
-  if (!is.null(graph$coordinates)) {
-    dd = as.data.frame(graph$coordinates)
+  if (!is.null(x$coordinates)) {
+    dd = as.data.frame(x$coordinates)
     names(dd) = c("x1", "x2")
-    if (!is.null(graph$membership))
-      dd$Cluster = as.factor(graph$membership)
+    if (!is.null(x$membership))
+      dd$Cluster = as.factor(x$membership)
     pl.coords = ggplot2::ggplot(dd, aes_string(x = "x1", y = "x2"))
     pl.coords = if (n.clusters > 0L) pl.coords + 
       ggplot2::geom_point(aes_string(colour = "Cluster")) else pl.coords + ggplot2::geom_point()
     if (n.clusters > 0L & show.cluster.centers) {
-      ddc = as.data.frame(graph$center.coordinates)
+      ddc = as.data.frame(x$center.coordinates)
       names(ddc) = c("x1", "x2")
       pl.coords = pl.coords + 
         ggplot2::geom_point(data = ddc, colour = "black", size = 3)
@@ -49,16 +49,16 @@ plot.mcGP = function(graph, show.cluster.centers = TRUE, x=NULL, y=NULL, ...) {
       ggplot2::xlab(expression(x[1])) + 
       ggplot2::ylab(expression(x[2]))
   }
-  weights1 = graph$weights[[1L]]
-  weights2 = graph$weights[[2L]]
+  weights1 = x$weights[[1L]]
+  weights2 = x$weights[[2L]]
 
   weights1 = as.numeric(weights1[upper.tri(weights1)])
   weights2 = as.numeric(weights2[upper.tri(weights2)])
 
   dd = data.frame(w1 = weights1, w2 = weights2)
   pl.weights = ggplot2::ggplot(dd, aes_string(x = "w1", y = "w2")) + ggplot2::geom_point()
   pl.weights = pl.weights + 
-    ggplot2::ggtitle("Edge weights", subtitle = collapse(paste(names(dd), graph$weight.types, sep = " : "), sep = ","))
+    ggplot2::ggtitle("Edge weights", subtitle = collapse(paste(names(dd), x$weight.types, sep = " : "), sep = ","))
   pl.weights = pl.weights + xlab(expression(w[1])) + ylab(expression(w[2]))