merge_density_foldchange: Create high-density region plot with optional points, density...

In TransProR: Analysis and Visualization of Multi-Omics Data

Create high-density region plot with optional points, density rugs, and contours

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.

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

data	Data frame containing variables for plotting.
x_var	Name of the x-axis variable as a string.
y_var	Name of the y-axis variable as a string.
group_var	Name of the grouping variable for color mapping as a string.
palette	Color palette for the plot as a character vector.
show_points	Logical, if TRUE adds points to the plot.
point_size	Size of the points, relevant if show_points is TRUE.
point_alpha	Transparency level of the points, relevant if show_points is TRUE.
x_lim	Numeric vector of length 2, giving the x-axis limits.
y_lim	Numeric vector of length 2, giving the y-axis limits.
cor_method	Method to calculate correlation ("pearson" or "spearman").
line_size	Size of the smoothing line.
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.

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")
)

TransProR documentation built on April 4, 2025, 3:16 a.m.