--- a
+++ b/man/create_base_plot.Rd
@@ -0,0 +1,60 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CircosFruits.R
+\name{create_base_plot}
+\alias{create_base_plot}
+\title{Create a base plot with gene expression data on a phylogenetic tree}
+\usage{
+create_base_plot(p, data, gene_colors, gene_label = "Gene")
+}
+\arguments{
+\item{p}{A ggtree plot object to which the data will be added.}
+
+\item{data}{A data frame containing gene expression data with columns for Samples, Genes, and Values.}
+
+\item{gene_colors}{A named vector of colors for genes.}
+
+\item{gene_label}{A character string used as a label in the legend for the genes. Default is "Gene".}
+}
+\value{
+A `ggtree` plot object with the gene expression data added.
+}
+\description{
+This function creates a base plot using 'ggtree' and 'ggtreeExtra' libraries, adding gene expression
+data as colored tiles to the plot. It allows for dynamic coloring of the genes and includes
+adjustments for alpha transparency based on the expression value.
+}
+\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 gene expression data frame
+  expression_data <- data.frame(
+    Sample = rep(c("Species_A", "Species_B", "Species_C", "Species_D"), each = 5),
+    Gene = rep(paste0("Gene", 1:5), times = 4),
+    Value = runif(20, min = 0, max = 1)  # Randomly generate expression values between 0 and 1
+  )
+
+  # Define gene colors (named vector)
+  gene_colors <- c(
+    Gene1 = "#491588",
+    Gene2 = "#301b8d",
+    Gene3 = "#1a237a",
+    Gene4 = "#11479c",
+    Gene5 = "#0a5797"
+  )
+
+  # Call create_base_plot function to add gene expression data
+  p <- create_base_plot(p, expression_data, gene_colors)
+} else {
+  message("Required packages 'ggtreeExtra' and 'ggplot2' are not installed.")
+}
+}
+
+}