flex_interval: flex_interval function

In GPflexViz: Graphical Visualizations Related to Genomic Prediction

flex_interval function

Description

This function visualizes individual polygenic risk scores (PRS) with corresponding confidence intervals. It supports customization of reference lines, colors, themes, and interactivity.

Usage

flex_interval(
  CI_data,
  user_ref_line = NULL,
  user_ref_color = "red",
  user_ref_linetype = "dashed",
  user_ref_visible = TRUE,
  user_point_color = "blue",
  user_point_size = 3,
  user_errorbar_color = "black",
  user_errorbar_size = 0.2,
  interactive = TRUE,
  user_theme = theme_minimal(),
  user_theme_specifications = theme(),
  user_title = "PRS with Confidence Intervals",
  user_x_label = "Individual",
  user_y_label = "Polygenic Risk Score (PRS)"
)

Arguments

CI_data	Data frame containing columns: IID, PRS, Variance, Lower_Limit, and Upper_Limit.
user_ref_line	Numeric or vector. Horizontal reference line(s) to be added. If NULL, defaults to mean PRS. Default is NULL.
user_ref_color	Character or vector. Color(s) of reference line(s). Default is "red".
user_ref_linetype	Character or vector. Linetype(s) for reference line(s). Default is "dashed".
user_ref_visible	Logical. Whether to display the reference line(s). Default is TRUE.
user_point_color	Character. Color of PRS points. Default is "blue".
user_point_size	Numeric. Size of PRS points. Default is 3.
user_errorbar_color	Character. Color of confidence interval error bars. Default is "black".
user_errorbar_size	Numeric. Width of error bars. Default is 0.2.
interactive	Logical. If TRUE, returns an interactive plot using plotly. Default is TRUE.
user_theme	A ggplot2 theme object. Default is theme_minimal().
user_theme_specifications	Additional theme specifications. Default is an empty theme() object.
user_title	Character. Title of the plot. Default is "PRS with Confidence Intervals".
user_x_label	Character. X-axis label. Default is "Individual".
user_y_label	Character. Y-axis label. Default is "Polygenic Risk Score (PRS)".

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)
set.seed(123)
example_data <- data.frame(
  IID = paste0("ID_", 1:8),
  PRS = rnorm(8, 0, 1),
  Variance = runif(8, 0.01, 0.1)
)
example_data$Lower_Limit <- example_data$PRS - 1.96 * sqrt(example_data$Variance)
example_data$Upper_Limit <- example_data$PRS + 1.96 * sqrt(example_data$Variance)
CI_data <- example_data

# Basic 
flex_interval(CI_data)

# Add custom reference lines
flex_interval(CI_data,
             user_ref_line = c(1, -1),
             user_ref_color = c("darkgreen", "darkred"),
             user_ref_linetype = c("dotted", "twodash"))

# Static plot with theme customization
flex_interval(CI_data, interactive = FALSE,
             user_theme_specifications = theme(axis.text.x = element_text(angle = 45, hjust = 1)),
             user_point_color = "magenta",
             user_errorbar_color = "darkred")

# Sorted PRS plot
ordered_data <- CI_data[order(-CI_data$PRS),]
ordered_data$IID <- factor(ordered_data$IID, levels = ordered_data$IID)
flex_interval(ordered_data, interactive = FALSE, user_ref_visible = FALSE)

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