--- a
+++ b/man/add_new_tile_layer.Rd
@@ -0,0 +1,86 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CircosFruits.R
+\name{add_new_tile_layer}
+\alias{add_new_tile_layer}
+\title{Add a new tile layer with dynamic scales to a `ggtree` plot}
+\usage{
+add_new_tile_layer(
+  p,
+  data,
+  gene_colors,
+  gene_label,
+  alpha_value = c(0.3, 0.9),
+  offset = 0.02,
+  pwidth = 2
+)
+}
+\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', 'Gene', and 'value'.}
+
+\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.}
+
+\item{alpha_value}{A numeric or named vector for setting the alpha scale based on values.}
+
+\item{offset}{Numeric value, the position of the tile on the x-axis relative to its gene name. Default is 0.02.}
+
+\item{pwidth}{Numeric value, the width of the tile. Default is 2.}
+}
+\value{
+A `ggtree` plot object with the added tile layer and new scales.
+}
+\description{
+This function adds a new tile layer to an existing `ggtree` plot object, allowing for separate scales for fill
+and alpha transparency. This is useful when you want to add additional data layers without interfering with
+the existing scales in the plot. It utilizes the 'ggnewscale' package to reset scales for new layers.
+}
+\examples{
+\donttest{
+# Check and load required packages
+if (requireNamespace("ggtreeExtra", quietly = TRUE) &&
+ requireNamespace("ggplot2", quietly = TRUE) &&
+  requireNamespace("ggnewscale", quietly = TRUE)) {
+  library(ggtreeExtra)
+  library(ggplot2)
+  library(ggnewscale)
+
+  file_path <- system.file("extdata", "p_tree_test.rds", package = "TransProR")
+  p <- readRDS(file_path)
+
+  # Create new expression data
+  new_expression_data <- data.frame(
+    Sample = rep(c("Species_A", "Species_B", "Species_C", "Species_D"), each = 3),
+    Gene = rep(c("Gene6", "Gene7", "Gene8"), times = 4),
+    Value = runif(12, min = 0, max = 1)  # Randomly generate expression values between 0 and 1
+  )
+
+  # Define new gene colors
+  new_gene_colors <- c(
+    Gene6 = "#0b5f63",
+    Gene7 = "#074d41",
+    Gene8 = "#1f5e27"
+  )
+
+  # Define gene label and alpha values
+  gene_label <- "New Genes"
+  alpha_value <- c(0.3, 0.9)
+
+  # Add new tile layer
+  p_with_new_layer <- add_new_tile_layer(
+    p,
+    new_expression_data,
+    new_gene_colors,
+    gene_label,
+    alpha_value,
+    offset = 0.02,
+    pwidth = 2
+  )
+} else {
+  message("Required packages 'ggtreeExtra', 'ggplot2', and 'ggnewscale' are not installed.")
+}
+}
+
+}