--- a
+++ b/man/circos_fruits.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CircosFruits.R
+\name{circos_fruits}
+\alias{circos_fruits}
+\title{Add multiple layers to a `ggtree` plot for visualizing gene expression and enrichment data}
+\usage{
+circos_fruits(
+  p,
+  long_format_HeatdataDeseq,
+  ssgsea_kegg_HeatdataDeseq,
+  gsva_kegg_HeatdataDeseq,
+  gene_colors
+)
+}
+\arguments{
+\item{p}{A `ggtree` plot object to which the data and layers will be added.}
+
+\item{long_format_HeatdataDeseq}{A data frame containing gene expression data with columns for `Samples`, `Genes`, and `Values`.}
+
+\item{ssgsea_kegg_HeatdataDeseq}{A data frame containing SSGSEA analysis results with columns for `Samples`, `Genes`, and `Values`.}
+
+\item{gsva_kegg_HeatdataDeseq}{A data frame containing GSVA analysis results with columns for `Samples`, `Genes`, and `Values`.}
+
+\item{gene_colors}{A named vector of colors for genes, used for coloring tiles in different layers.}
+}
+\value{
+A `ggtree` plot object with multiple layers added for comprehensive visualization.
+}
+\description{
+This function sequentially adds multiple layers to a `ggtree` plot, including gene expression data, boxplots for statistical
+summaries, and additional tile layers for pathway enrichment scores from SSGSEA and GSVA analyses. It utilizes separate
+functions for adding each type of layer and allows for the specification of gene colors as well as adjustments in aesthetics
+for each layer. The function is designed to work with specific data structures and assumes all functions for adding layers
+are defined and available.
+}
+\examples{
+\donttest{
+# Check and load required packages
+if (requireNamespace("ggtreeExtra", quietly = TRUE) &&
+ requireNamespace("ggplot2", quietly = TRUE)) {
+  library(ggtreeExtra)
+  library(ggplot2)
+
+  # Example data for gene expression, SSGSEA, and GSVA
+  file_path <- system.file("extdata", "p_tree_test.rds", package = "TransProR")
+  p <- readRDS(file_path)
+
+  # Create gene expression data frame (long_format_HeatdataDeseq)
+  long_format_HeatdataDeseq <- data.frame(
+    Sample = rep(c("Species_A", "Species_B", "Species_C", "Species_D"), each = 5),
+    Genes = rep(paste0("Gene", 1:5), times = 4),
+    Value = runif(20, min = 0, max = 1)  # Randomly generate expression values between 0 and 1
+  )
+
+  # Create SSGSEA analysis results data frame (ssgsea_kegg_HeatdataDeseq)
+  ssgsea_kegg_HeatdataDeseq <- data.frame(
+    Sample = rep(c("Species_A", "Species_B", "Species_C", "Species_D"), each = 3),
+    Genes = rep(c("Pathway1", "Pathway2", "Pathway3"), times = 4),
+    Value = runif(12, min = 0, max = 1)  # Randomly generate enrichment scores between 0 and 1
+  )
+
+  # Create GSVA analysis results data frame (gsva_kegg_HeatdataDeseq)
+  gsva_kegg_HeatdataDeseq <- data.frame(
+    Sample = rep(c("Species_A", "Species_B", "Species_C", "Species_D"), each = 4),
+    Genes = rep(c("PathwayA", "PathwayB", "PathwayC", "PathwayD"), times = 4),
+    Value = runif(16, min = 0, max = 1)  # Randomly generate enrichment scores between 0 and 1
+  )
+
+  # Define gene and pathway colors (named vector), including all genes and pathways
+  gene_colors <- c(
+    # Genes for gene expression
+    Gene1 = "#491588",
+    Gene2 = "#301b8d",
+    Gene3 = "#1a237a",
+    Gene4 = "#11479c",
+    Gene5 = "#0a5797",
+    # Pathways for SSGSEA
+    Pathway1 = "#0b5f63",
+    Pathway2 = "#074d41",
+    Pathway3 = "#1f5e27",
+    # Pathways for GSVA
+    PathwayA = "#366928",
+    PathwayB = "#827729",
+    PathwayC = "#a1d99b",
+    PathwayD = "#c7e9c0"
+  )
+
+  # Call circos_fruits function to add multiple layers
+  final_plot <- circos_fruits(
+    p,
+    long_format_HeatdataDeseq,
+    ssgsea_kegg_HeatdataDeseq,
+    gsva_kegg_HeatdataDeseq,
+    gene_colors
+  )
+} else {
+  message("Required packages 'ggtreeExtra' and 'ggplot2' are not installed.")
+}
+}
+
+}