% 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.")

}

}

}