flex_accuracy_diff: flex_accuracy_diff function

In GPflexViz: Graphical Visualizations Related to Genomic Prediction

flex_accuracy_diff function

Description

This function generates a customizable bar plot to compare prediction accuracy (e.g. R-squared values) between multiple models. It displays pairwise comparison lines and corresponding p-values. Interactive plots can be created using Plotly.

Usage

flex_accuracy_diff(
  accuracy_data,
  comparison_data,
  interactive = TRUE,
  user_colors = NULL,
  user_segment_color = "darkblue",
  display_p_values = TRUE,
  models_to_display_p_values = NULL,
  user_title = "Prediction Accuracy Comparison Plot",
  user_x_title = "Model",
  user_y_title = "Prediction Accuracy",
  user_legend_title = NULL,
  user_plot_theme = theme_minimal(),
  user_plot_theme_specs = theme(legend.title = element_text(size = 10), legend.text =
    element_text(size = 15), 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_p_value_prefix = NULL,
  user_bar_width = 0.8,
  geom_text_args = list(),
  additional_ggplot_args = list()
)

Arguments

accuracy_data	A data frame containing the models' R-squared values with two columns: 'Model' and 'R_squared'
comparison_data	A data frame containing pairwise comparisons with three columns: 'Compare1', 'Compare2' and 'p_value'
interactive	Logical. If 'TRUE', returns an interactive plotly object; otherwise, returns a static ggplot object. Default is 'TRUE'.
user_colors	Character vector of colors for the bars. If 'NULL', uses ggplot2 default colors. Default is 'NULL'.
user_segment_color	Character. Color of comparison lines and dashed segments. Default is "darkblue"'.
display_p_values	Logical. If 'TRUE', adds p-values to the plot for specified comparisons. Default is 'TRUE'.
models_to_display_p_values	Character vector of model pairs for which p-values should be displayed, formatted as "Model1 Model2"'. Default is 'NULL'.
user_title	Character. Title of the plot. Default is "Prediction Accuracy Comparison Plot"'.
user_x_title	Character. Title of the x-axis. Default is "Model"'.
user_y_title	Character. Title of the y-axis. Default is "Prediction Accuracy"'.
user_legend_title	Character. Title of the legend. Default is 'NULL'.
user_plot_theme	A ggplot2 theme to be applied to the plot. Default is 'theme_minimal()'.
user_plot_theme_specs	Additional theme specifications applied after 'user_plot_theme'. Default is a set of predefined theme customizations.
user_p_value_prefix	Character. Prefix to be added before displaying p-values. Default is 'NULL'.
user_bar_width	Numeric. Width of the bars. Default is '0.8'.
geom_text_args	List. Additional arguments for 'geom_text', such as color, font size, or angle. Default is an empty list.
additional_ggplot_args	List. Additional ggplot2 layers or arguments to be added to the plot. Default is an empty list.

Value

A ggplot object if 'interactive' is FALSE; otherwise, an interactive Plotly plot.

Examples

library(ggplot2)
library(plotly)
library(dplyr)
library(nortest)
library(ggforce)
library(reshape2)
library(gridExtra)
library(grid)
library(cowplot)
accuracy_data <- example_data4
comparison_data <- example_data5
# Create a static plot
flex_accuracy_diff(accuracy_data, comparison_data, interactive = FALSE)

# Create an interactive plot
flex_accuracy_diff(accuracy_data, comparison_data)

# Display specific p-values
flex_accuracy_diff(accuracy_data, comparison_data, 
  models_to_display_p_values = c("Model A Model B"))

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