flex_LD_decay: flex_LD_decay function

In GPflexViz: Graphical Visualizations Related to Genomic Prediction

flex_LD_decay function

Description

This function generates a linkage disequilibrium (LD) decay plot based on input LD data. It supports both static and interactive visualization with customizable aesthetics, themes, and optional smoothing curves.

Usage

flex_LD_decay(
  ld_data,
  interactive = TRUE,
  user_colors = NULL,
  user_title = "LD Decay Plot",
  user_x_title = "Distance (Mb)",
  user_y_title = "R-squared (LD)",
  user_legend_title = "Chromosome",
  user_plot_theme = theme_minimal(),
  user_plot_theme_specs = theme(legend.title = element_text(size = 10), legend.text =
    element_text(size = 10), title = element_text(size = 15), axis.text.x =
    element_text(size = 10), axis.title.x = element_text(size = 10), axis.text.y =
    element_text(size = 10), axis.title.y = element_text(size = 10)),
  user_base = 1e+06,
  user_smoothing = "loess",
  add_smoothing = FALSE,
  add_smoothing_per_chromosome = FALSE,
  ...
)

Arguments

ld_data	Data frame containing LD information.
interactive	Logical. If TRUE, returns an interactive plot using plotly. Default is TRUE.
user_colors	Character vector of colors for chromosomes. If NULL, default colors are used. Default is NULL.
user_title	Character. Title of the plot. Default is "LD Decay Plot".
user_x_title	Character. X-axis label. Default is "Distance (Mb)".
user_y_title	Character. Y-axis label. Default is "R-squared (LD)".
user_legend_title	Character. Legend title. Default is "Chromosome".
user_plot_theme	A ggplot2 theme object. Default is theme_minimal().
user_plot_theme_specs	Additional theme specifications applied to the plot. Default is a theme object with custom font sizes.
user_base	Numeric. Scaling factor for distance (e.g., 1e6 for Mb). Default is 1e6.
user_smoothing	Character. Smoothing method to use in geom_smooth. Default is "loess".
add_smoothing	Logical. If TRUE, adds a smoothing curve to the plot. Default is FALSE.
add_smoothing_per_chromosome	Logical. If TRUE, adds separate smoothing curves for each chromosome. Default is FALSE.
...	Additional arguments passed to geom_smooth (e.g., span, se, etc.).

Value

A ggplot object (static plot) or a plotly object (interactive plot), depending on the value of interactive.

Examples

library(ggplot2)
library(plotly)
library(dplyr)
library(nortest)
library(ggforce)
library(reshape2)
library(gridExtra)
library(grid)
library(cowplot)
# Load example data
snp_ld_data <- example_data7

# Basic plot
flex_LD_decay(snp_ld_data)

# Add a general smoothing curve
flex_LD_decay(snp_ld_data, add_smoothing = TRUE)

# Add smoothing per chromosome
flex_LD_decay(snp_ld_data, add_smoothing = TRUE, add_smoothing_per_chromosome = TRUE)

# Customize smoothing parameters
flex_LD_decay(snp_ld_data, add_smoothing = TRUE, span = 0.5, se = FALSE)

# Use generalized additive model (GAM) for smoothing
flex_LD_decay(snp_ld_data, user_smoothing = "gam", add_smoothing = TRUE, 
add_smoothing_per_chromosome = TRUE)

GPflexViz documentation built on Sept. 10, 2025, 10:27 a.m.