--- a
+++ b/R/HighlightByNode.R
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+#' Highlight Nodes in a Phylogenetic Tree with Custom Fill Colors and Transparency
+#'
+#' This function adds highlights to specific nodes in a phylogenetic tree represented by a `ggtree` object.
+#' Users can specify the nodes to highlight along with custom fill colors, transparency, and extension options.
+#'
+#' @importFrom ggtree geom_hilight
+#' @param ggtree_object A `ggtree` object representing the phylogenetic tree.
+#' @param nodes A character vector specifying the nodes to highlight.
+#' @param fill_colors A character vector specifying the fill colors for the highlighted nodes.
+#' @param alpha_values A numeric vector specifying the transparency values for the highlighted nodes (between 0 and 1).
+#' @param extend_values A logical vector specifying whether to extend the highlight to the whole clade below each node.
+#' @return A modified `ggtree` object with the specified nodes highlighted.
+#' @export
+#'
+#' @examples
+#' plot_file <- system.file("extdata", "tree_plot.rds", package = "TransProR")
+#' p2_plot <- readRDS(plot_file)
+#'
+#' # Please replace the following vectors with your specific values
+#' nodes <- c(117, 129, 125, 127, 119,
+#'            123, 139, 166, 124, 131, 217) # x-values of the nodes you want to highlight
+#' fill_colors <- c("#CD6600", "#CD6600", "#CD6600",
+#'                  "#CD6600", "#009933", "#009933",
+#'                  "#009933", "#009933", "#9B30FF",
+#'                  "#9B30FF", "#9B30FF") # Fill colors
+#' alpha_values <- c(0.3, 0.3, 0.3, 0.3, 0.2, 0.3,
+#'                   0.3, 0.3, 0.3, 0.3, 0.3) # Transparency values
+#' extend_values <- c(25, 24, 24, 25, 25, 25,
+#'                    24, 24, 25, 24, 24) # Values for the 'extend' parameter
+#'
+#' p2 <- highlight_by_node(
+#'   p2_plot,
+#'   nodes,
+#'   fill_colors,
+#'   alpha_values,
+#'   extend_values
+#' )
+highlight_by_node <- function(ggtree_object,
+                              nodes,
+                              fill_colors,
+                              alpha_values,
+                              extend_values) {
+  # Ensure that the lengths of `nodes`, `fill_colors`, `alpha_values`, and `extend_values` are consistent
+  if (!(length(nodes) == length(fill_colors) && length(nodes) == length(alpha_values) && length(nodes) == length(extend_values))) {
+    stop("Length of nodes, fill_colors, alpha_values, and extend_values must be the same.")
+  }
+
+  if (!requireNamespace("systemfonts", quietly = TRUE)) {
+    stop("ggplot2 is required to use the function. Please install it.", call. = FALSE)
+  }
+
+  # For each node, add the corresponding geom_hilight layer
+  layers <- lapply(seq_along(nodes), function(i) {
+    node <- nodes[i]
+    fill_color <- fill_colors[i]
+    alpha_val <- alpha_values[i]
+    extend_val <- extend_values[i]
+
+    # Create a geom_hilight layer
+    ggtree::geom_hilight(node = node, fill = fill_color, alpha = alpha_val, extend = extend_val)
+  })
+
+  # Add all layers to the `ggtree` object
+  for (layer in layers) {
+    ggtree_object <- ggtree_object + layer
+  }
+
+  return(ggtree_object)
+}