add_boxplot: Add a boxplot layer to a 'ggtree' plot

In TransProR: Analysis and Visualization of Multi-Omics Data

Add a boxplot layer to a 'ggtree' plot

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.

Usage

add_boxplot(
  p,
  data,
  fill_color = "#f28131",
  alpha = 0.6,
  offset = 0.22,
  pwidth = 0.5
)

Arguments

p	An existing ggtree plot object.
data	A data frame containing the data to be plotted. Expected to have columns for 'Sample' and 'value'.
fill_color	A character string specifying the fill color for the boxplots. Default is "#f28131".
alpha	Numeric value for the transparency of the boxplots. Default is 0.6.
offset	Numeric value, the position of the boxplot on the x-axis relative to its gene name. Default is 0.22.
pwidth	Numeric value, the width of the boxplot. Default is 0.5.

Value

A 'ggtree' plot object with the added boxplot layer.

Examples

# 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.")
}

TransProR documentation built on April 4, 2025, 3:16 a.m.