--- a
+++ b/man/facet_density_foldchange.Rd
@@ -0,0 +1,81 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/FacetDensityFoldchange.R
+\name{facet_density_foldchange}
+\alias{facet_density_foldchange}
+\title{Create faceted high-density region plots with optional points and density contours}
+\usage{
+facet_density_foldchange(
+  data,
+  x_var,
+  y_var,
+  group_var,
+  facet_var,
+  palette,
+  show_points = FALSE,
+  show_density = TRUE,
+  point_size = 2.5,
+  point_alpha = 0.1,
+  line_size = 1.6,
+  cor_method = "pearson",
+  cor_label_pos = c("left", 0.97),
+  cor_vjust = NULL
+)
+}
+\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{facet_var}{Name of the faceting variable.}
+
+\item{palette}{Color palette for the plot as a character vector.}
+
+\item{show_points}{Logical, if TRUE adds scatter points to the plot.}
+
+\item{show_density}{Logical, if TRUE adds filled density contours 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{line_size}{Size of the regression line.}
+
+\item{cor_method}{Method to calculate correlation ("pearson" or "spearman").}
+
+\item{cor_label_pos}{Vector of length 2 indicating the position of the correlation label (x and y).}
+
+\item{cor_vjust}{Vertical justification for correlation label, default is NULL.}
+}
+\value{
+A `ggplot` object representing the high-density region plot.
+}
+\description{
+This function creates faceted high-density region plots using ggdensity for
+adding optional density rug and density contours, and scatter points. It also adds a regression line
+and Pearson correlation label. The plot is faceted by a grouping variable.
+}
+\examples{
+combined_df_file <- system.file("extdata", "combined_df.rds", package = "TransProR")
+combined_df <- readRDS(combined_df_file)
+pal2 = c("#2787e0","#1a9ae0","#1dabbf","#00897b","#43a047","#7cb342")
+all_facet_density_foldchange_name1 <- facet_density_foldchange(
+  data = combined_df,
+  x_var = "log2FoldChange_1",
+  y_var = "log2FoldChange_2",
+  group_var = "name",
+  facet_var = "name",
+  palette = pal2,
+  show_points = TRUE,
+  show_density = FALSE,
+  point_size = 2,
+  point_alpha = 0.1,
+  line_size = 1.6,
+  cor_method = "pearson",
+  cor_label_pos = c("left", "top"),
+  cor_vjust = 1
+)
+}