--- a
+++ b/man/add_boxplot.Rd
@@ -0,0 +1,65 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CircosFruits.R
+\name{add_boxplot}
+\alias{add_boxplot}
+\title{Add a boxplot layer to a `ggtree` plot}
+\usage{
+add_boxplot(
+  p,
+  data,
+  fill_color = "#f28131",
+  alpha = 0.6,
+  offset = 0.22,
+  pwidth = 0.5
+)
+}
+\arguments{
+\item{p}{An existing ggtree plot object.}
+
+\item{data}{A data frame containing the data to be plotted. Expected to have columns for 'Sample' and 'value'.}
+
+\item{fill_color}{A character string specifying the fill color for the boxplots. Default is "#f28131".}
+
+\item{alpha}{Numeric value for the transparency of the boxplots. Default is 0.6.}
+
+\item{offset}{Numeric value, the position of the boxplot on the x-axis relative to its gene name. Default is 0.22.}
+
+\item{pwidth}{Numeric value, the width of the boxplot. Default is 0.5.}
+}
+\value{
+A `ggtree` plot object with the added boxplot layer.
+}
+\description{
+This function adds a boxplot layer to an existing `ggtree` plot object using ggtreeExtra's geom_fruit for boxplots.
+It is primarily used to display statistical summaries of the data related to gene expressions or other metrics.
+}
+\examples{
+\donttest{
+# Check and load required packages
+if (requireNamespace("ggtreeExtra", quietly = TRUE) &&
+ requireNamespace("ggplot2", quietly = TRUE)) {
+  library(ggtreeExtra)
+  library(ggplot2)
+
+  file_path <- system.file("extdata", "p_tree_test.rds", package = "TransProR")
+  p <- readRDS(file_path)
+
+  # Create boxplot data frame
+  boxplot_data <- data.frame(
+    Sample = rep(c("Species_A", "Species_B", "Species_C", "Species_D"), each = 30),
+    value = c(
+      rnorm(30, mean = 5, sd = 1),   # Data for Species_A
+      rnorm(30, mean = 7, sd = 1.5), # Data for Species_B
+      rnorm(30, mean = 6, sd = 1.2), # Data for Species_C
+      rnorm(30, mean = 8, sd = 1.3)  # Data for Species_D
+    )
+  )
+
+  # Call add_boxplot function to add boxplot layer
+  p_with_boxplot <- add_boxplot(p, boxplot_data)
+} else {
+  message("Required packages 'ggtreeExtra' and 'ggplot2' are not installed.")
+}
+}
+
+}