flex_accuracy_diff2: flex_accuracy_diff2 function

In GPflexViz: Graphical Visualizations Related to Genomic Prediction

flex_accuracy_diff2 function

Description

This function generates detailed interactive or static visualizations comparing the accuracy of two methods across different traits. It uses ggplot2 and plotly for rendering the plots.

Usage

flex_accuracy_diff2(
  accuracy_diff_data,
  user_colors = c("lightblue", "lightpink"),
  interactive = TRUE,
  user_geom_bar = geom_bar(stat = "identity", position = position_dodge(0.5), width =
    0.4),
  user_geom_point = geom_point(aes(x = trait, y = R2diff), color = "black", size = 2),
  user_accuracy_geom_errorbar = geom_errorbar(aes(ymin = lower_limit_R2, ymax =
    upper_limit_R2), color = "black", width = 0.1, position = position_dodge(0.5)),
  user_accuracy_diff_geom_errorbar = geom_errorbar(width = 0.05, color = "black"),
  user_geom_text = geom_text(aes(x = trait, y = ymax + 0.1, label = p_value), hjust =
    0.5, size = 3.5),
  user_ylim_accuracy = ylim(0, 1),
  user_ylim_accuracy_difference = ylim(0, 1),
  user_accuracy_labs = labs(x = "", y = "R2", title = "R2 values"),
  user_accuracy_diff_labs = labs(x = "", y = "Difference", title =
    "Difference between R2"),
  user_accuracy_theme = theme_minimal(),
  user_accuracy_diff_theme = theme_minimal(),
  user_accuracy_theme_specs = theme(legend.position = c(0.85, 0.85)),
  user_accuracy_diff_theme_specs = theme(axis.title.x = element_blank(), axis.text.x =
    element_blank(), axis.ticks.x = element_blank(), plot.margin = unit(c(1, 1, 1, 1),
    "lines"))
)

Arguments

accuracy_diff_data	A data frame containing nine columns and at least two rows: trait (factor or character vector of trait names), method (factor or character vector of method names (two methods)), R2 (numeric vector of accuracy of the methods for a trait), lower_limit_R2 (numeric vector of lower limits of accuracy), upper_limit_R2 (numeric vector of upper limits of accuracy), difference_R2 (numeric vector of differences between the methods' accuracies), lower_limit_difference_R2 (numeric vector of lower limits of differences in accuracies), upper_limit_difference_R2 (numeric vector of upper limits of differences in accuracies), and p_value_difference_R2 (numeric vector of p-values for differences in accuracies).
user_colors	A character vector of length 2 specifying colors for the two methods in the bar plot.
interactive	Logical, if TRUE the function returns an interactive plotly plot, otherwise it returns a ggplot object.
user_geom_bar	A ggplot2 geom_bar object for customizing the bar plot appearance. Accepts parameters like stat, position, and width to control the visual properties of the bars.
user_geom_point	A ggplot2 geom_point object for customizing the point plot appearance. This includes settings for color and size of points which represent the differences in accuracy.
user_accuracy_geom_errorbar	A ggplot2 geom_errorbar object for customizing the error bars in the accuracy plot. This involves setting parameters like color, width, and position to visually modify how error bars are displayed.
user_accuracy_diff_geom_errorbar	A ggplot2 geom_errorbar object for customizing the error bars in the accuracy difference plot. Similar to user_accuracy_geom_errorbar, but typically used to emphasize differences between methods.
user_geom_text	A ggplot2 geom_text object for adding text annotations to the plots. This can include parameters for positioning, size, and the label content, often used to display statistical significance or other annotations.
user_ylim_accuracy	A ggplot2 ylim function call for setting the y-axis limits in the accuracy plot. This helps in controlling the scale of the plot to better fit the data presentation.
user_ylim_accuracy_difference	A ggplot2 ylim function call for setting the y-axis limits in the accuracy difference plot. Useful for maintaining consistent visual scales across related plots.
user_accuracy_labs	A ggplot2 labs function call for setting labels and titles in the accuracy plot. This includes parameters to set the x-axis label, y-axis label, and the main title of the plot.
user_accuracy_diff_labs	A ggplot2 labs function call for setting labels and titles in the accuracy difference plot. Useful for distinguishing between different plots and providing clear, informative titles and labels.
user_accuracy_theme	A ggplot2 theme object for applying styling themes to the accuracy plot. This parameter can be used to apply a predefined theme or customize aspects like text, background, and grid lines.
user_accuracy_diff_theme	A ggplot2 theme object for applying styling themes to the accuracy difference plot. Allows for consistent or contrasting styles between different types of visualizations in the package.
user_accuracy_theme_specs	Additional ggplot2 theme modifications specifically for the accuracy plot. This can involve finer control over elements like legend position and plot margins.
user_accuracy_diff_theme_specs	Additional ggplot2 theme modifications specifically for the accuracy difference plot. Tailored to enhance or modify specific aspects of the plot's appearance beyond the base theme settings.

Value

Either a ggplot or plotly object depending on the interactive argument.

Examples

library(ggplot2)
library(plotly)
library(dplyr)
library(nortest)
library(ggforce)
library(reshape2)
library(gridExtra)
library(grid)
library(cowplot)
flex_accuracy_diff2(example_data6)

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