facet_density_foldchange: Create faceted high-density region plots with optional points...

In TransProR: Analysis and Visualization of Multi-Omics Data

Create faceted high-density region plots with optional points and density contours

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.

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

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.
facet_var	Name of the faceting variable.
palette	Color palette for the plot as a character vector.
show_points	Logical, if TRUE adds scatter points to the plot.
show_density	Logical, if TRUE adds filled density contours 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.
line_size	Size of the regression line.
cor_method	Method to calculate correlation ("pearson" or "spearman").
cor_label_pos	Vector of length 2 indicating the position of the correlation label (x and y).
cor_vjust	Vertical justification for correlation label, default is NULL.

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)
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
)

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