--- a
+++ b/man/merge_density_foldchange.Rd
@@ -0,0 +1,79 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MergeDensityFoldchange.R
+\name{merge_density_foldchange}
+\alias{merge_density_foldchange}
+\title{Create high-density region plot with optional points, density rugs, and contours}
+\usage{
+merge_density_foldchange(
+  data,
+  x_var,
+  y_var,
+  group_var,
+  palette = c("#3949ab", "#1e88e5", "#039be5", "#00897b", "#43a047", "#7cb342"),
+  show_points = FALSE,
+  point_size = 2.5,
+  point_alpha = 0.2,
+  x_lim = c(0, 20),
+  y_lim = c(0, 20),
+  cor_method = "pearson",
+  line_size = 1.6,
+  cor_label_pos = c("left", 0.97)
+)
+}
+\arguments{
+\item{data}{Data frame containing variables for plotting.}
+
+\item{x_var}{Name of the x-axis variable as a string.}
+
+\item{y_var}{Name of the y-axis variable as a string.}
+
+\item{group_var}{Name of the grouping variable for color mapping as a string.}
+
+\item{palette}{Color palette for the plot as a character vector.}
+
+\item{show_points}{Logical, if TRUE adds points to the plot.}
+
+\item{point_size}{Size of the points, relevant if show_points is TRUE.}
+
+\item{point_alpha}{Transparency level of the points, relevant if show_points is TRUE.}
+
+\item{x_lim}{Numeric vector of length 2, giving the x-axis limits.}
+
+\item{y_lim}{Numeric vector of length 2, giving the y-axis limits.}
+
+\item{cor_method}{Method to calculate correlation ("pearson" or "spearman").}
+
+\item{line_size}{Size of the smoothing line.}
+
+\item{cor_label_pos}{Vector of length 2 indicating the position of the correlation label (x and y).}
+}
+\value{
+A ggplot object representing the high-density region plot.
+}
+\description{
+This function creates a high-density region plot using hdr methods to
+add density rug and filled contours. It also adds a regression line
+and Pearson correlation label. Points can be added to the plot optionally.
+}
+\examples{
+combined_df_file <- system.file("extdata", "combined_df.rds", package = "TransProR")
+combined_df <- readRDS(combined_df_file)
+pal1 = c("#3949ab","#1e88e5","#039be5","#00897b","#43a047","#7cb342")
+
+all_density_foldchange_name1 <- merge_density_foldchange(
+  data = combined_df,
+  x_var = "log2FoldChange_1",
+  y_var = "log2FoldChange_2",
+  group_var = "name",
+  palette = pal1,
+  show_points = FALSE,
+  point_size = 2.5,
+  point_alpha = 0.1,
+  x_lim = c(0, 20),
+  y_lim = c(0, 20),
+  cor_method = "pearson",
+  line_size = 1.6,
+  cor_label_pos = c("left", "top")
+)
+
+}