--- a
+++ b/man/highlight_by_node.Rd
@@ -0,0 +1,56 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/HighlightByNode.R
+\name{highlight_by_node}
+\alias{highlight_by_node}
+\title{Highlight Nodes in a Phylogenetic Tree with Custom Fill Colors and Transparency}
+\usage{
+highlight_by_node(
+  ggtree_object,
+  nodes,
+  fill_colors,
+  alpha_values,
+  extend_values
+)
+}
+\arguments{
+\item{ggtree_object}{A `ggtree` object representing the phylogenetic tree.}
+
+\item{nodes}{A character vector specifying the nodes to highlight.}
+
+\item{fill_colors}{A character vector specifying the fill colors for the highlighted nodes.}
+
+\item{alpha_values}{A numeric vector specifying the transparency values for the highlighted nodes (between 0 and 1).}
+
+\item{extend_values}{A logical vector specifying whether to extend the highlight to the whole clade below each node.}
+}
+\value{
+A modified `ggtree` object with the specified nodes highlighted.
+}
+\description{
+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.
+}
+\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
+)
+}