--- a
+++ b/man/highlight_genes.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/HighlightGenes.R
+\name{highlight_genes}
+\alias{highlight_genes}
+\title{Add Highlights for Genes on a Phylogenetic Tree}
+\usage{
+highlight_genes(ggtree_obj, genes_to_highlight, hilight_extend = 18)
+}
+\arguments{
+\item{ggtree_obj}{A ggtree object representing the phylogenetic tree.}
+
+\item{genes_to_highlight}{A data frame containing gene names and corresponding colors to highlight.}
+
+\item{hilight_extend}{Numeric value indicating the extension length for highlights.}
+}
+\value{
+A `ggtree` object with added highlights for specified genes.
+}
+\description{
+This function adds highlights for specified genes on a phylogenetic tree object.
+}
+\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)
+}