#' 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)

}