--- a
+++ b/R/HighlightGenes.R
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+#' Add Highlights for Genes on a Phylogenetic Tree
+#'
+#' This function adds highlights for specified genes on a phylogenetic tree object.
+#'
+#' @importFrom ggtree geom_point2 geom_hilight aes
+#' @importFrom dplyr filter select pull
+#' @importFrom rlang .data
+#' @param ggtree_obj A ggtree object representing the phylogenetic tree.
+#' @param genes_to_highlight A data frame containing gene names and corresponding colors to highlight.
+#' @param hilight_extend Numeric value indicating the extension length for highlights.
+#' @return A `ggtree` object with added highlights for specified genes.
+#' @export
+#'
+#' @examples
+#' plot_file <- system.file("extdata", "tree_plot.rds", package = "TransProR")
+#' p2_plot <- readRDS(plot_file)
+#'
+#' selected_genes_deseq2_file <- system.file("extdata",
+#'                                           "selected_genes_deseq2.rds",
+#'                                           package = "TransProR")
+#' selected_genes_deseq2 <- readRDS(selected_genes_deseq2_file)
+#'
+#' Diff_deseq2_file <- system.file("extdata", "Diff_deseq2.rds", package = "TransProR")
+#' Diff_deseq2 <- readRDS(Diff_deseq2_file)
+#'
+#' result_deseq2 <- gene_color(selected_genes_deseq2, Diff_deseq2, "#0000EE", "#fc4746")
+#'
+#' add_gene_highlights_p3 <- highlight_genes(p2_plot, result_deseq2, hilight_extend = 26)
+highlight_genes <- function(ggtree_obj, genes_to_highlight, hilight_extend = 18) {
+  # Ensure that the first argument is a `ggtree` object
+  if (!inherits(ggtree_obj, "ggtree")) {
+    stop("The first argument must be a ggtree object.")
+  }
+
+  # Ensure that the second argument is a data frame
+  if (!("data.frame" %in% class(genes_to_highlight))) {
+    stop("The second argument must be a data frame.")
+  }
+
+  if (!requireNamespace("systemfonts", quietly = TRUE)) {
+    stop("ggplot2 is required to use the function. Please install it.", call. = FALSE)
+  }
+
+  # Extract the data from the tree object and ensure it is a data frame
+  tree_data <- as.data.frame(ggtree_obj$data)
+
+  # Map gene names and colors to nodes in the tree and create geom_hilight and geom_point2 layers for each node
+  highlight_commands <- lapply(1:nrow(genes_to_highlight), function(i) {
+    gene <- genes_to_highlight$Symble[i]
+    color <- genes_to_highlight$color[i]
+    node <- dplyr::filter(tree_data, .data$label == gene) %>%
+      dplyr::select(node) %>%
+      dplyr::pull()
+    if (!is.na(node)) {
+      list(
+        ggtree::geom_hilight(node = node, fill = color, alpha = 0.3, extend = hilight_extend),
+        ggtree::geom_point2(ggtree::aes(subset = (.data$label == gene)), color = color, size = 2, alpha = 0.6)
+      )
+    } else {
+      warning(paste("Gene", gene, "not found in the ggtree object."))
+      NULL
+    }
+  })
+
+  # Remove NULL elements from `highlight_commands` since they may exist
+  highlight_commands <- Filter(Negate(is.null), highlight_commands)
+
+  # Apply the commands to the `ggtree object`
+  ggtree_obj <- ggtree_obj + do.call(c, highlight_commands)
+
+  return(ggtree_obj)
+}