added dendrogram plot (still to do for basics)

R/plot_functions.R

 #' @import ggplot2
 #' @importFrom reshape2 melt
+#' @import dendextend
+#' @importFrom RColorBrewer brewer.pal
+
+plot_dendrogram <- function(x) {
+  
+  dendro <- as.dendrogram(x$dendro)
+  nlev <- dendextend::nleaves(dendro)
+  labs <- labels(dendro)
+  dendro <- set_labels(dendro, rep("", length(labs)))
+  dendro %>% plot(leaflab = "none") 
+  
+  all_at <- unique(x$mse$clust)
+  nrange <- length(x$groups)
+  kmax <- max(all_at)
+  # rectangles
+  dendro %>% rect.dendrogram(k = kmax)
+  
+  # horizontal lines ('range_at')
+  if (nrange > 1) {
+    all_h <- rev(x$dendro$height)
+    for (k in setdiff(all_at, max(all_at))) {
+      abline(h = (all_h[k] + all_h[k-1]) / 2, col = "darkred")
+    }
+  }
+  
+  if ("selected" %in% names(x)) { # case 'selected'
+    values <- replicate(nrange, rep("grey", length(labs)), simplify = FALSE)
+    values <- mapply(function(a, b) {
+      names(a) <- labs; a[b] <- "darkred"; return(a)
+      }, values, x$selected)
+    bar_labs <- paste("#int.:", names(x$groups), "- sel?")
+  } else {
+    best <- tapply(x$mse$mse, x$mse$clust, which.min)
+    values <- mapply(function(a, b) return(a[, b]), x$importances, best)
+    values <- apply(values, 2, cut, breaks = 9, labels = FALSE)
+    values <- apply(values, 2, function(acol) brewer.pal(9, "YlOrRd")[acol])
+    bar_labs <- paste("#int.:", names(x$groups), "- imp.")
+  }
+  # bars
+  colored_bars(colors = values, dend = dendro, rowLabels = bar_labs)
+
+  return(invisible(NULL))
+}
+
 plot_importance <- function(x, shape.imp) {
   lobj <- length(x$importances)
   nrepeats <- nrow(x$mse) / lobj