flex_qqplot: flex_qqplot function

In GPflexViz: Graphical Visualizations Related to Genomic Prediction

flex_qqplot function

Description

This function generates a customizable quantile-quantile (QQ) plot for GWAS data, allowing for interactive exploration, zooming on specific SNPs, and inclusion of a Kolmogorov-Smirnov test result annotation.

Usage

flex_qqplot(
  gwas_data,
  interactive = TRUE,
  display_ks = FALSE,
  user_colors = c("dodgerblue", "darkorange"),
  user_title = "QQ Plot",
  user_x_title = "Theoretical Quantiles",
  user_y_title = "Observed Quantiles",
  user_plot_theme = theme_minimal(),
  user_plot_theme_specs = theme(title = element_text(size = 15), axis.text =
    element_text(size = 10), axis.title = element_text(size = 10)),
  annotate_data = NULL,
  annotate_column = "SNP",
  annotate_labels = FALSE,
  zoom_on_annotations = FALSE,
  zoom_margin = 1,
  ...
)

Arguments

gwas_data	A data frame containing columns for SNP ID ('SNP’), chromosome ('CHR'), position ('POS'), and p-values ('P_VALUE').
interactive	Logical, whether to return an interactive plot (TRUE) or static ggplot (FALSE).
display_ks	Logical, whether to display the Kolmogorov-Smirnov (KS) test result.
user_colors	Character vector of length 2 specifying the colors for points and reference line.
user_title	The title of the plot.
user_x_title	The title for the x-axis.
user_y_title	The title for the y-axis.
user_plot_theme	A ggplot2 theme object to style the plot.
user_plot_theme_specs	Additional ggplot2 theme specifications to override in user_plot_theme.
annotate_data	A vector of SNP identifiers to annotate in the plot.
annotate_column	The name of the column in gwas_data to use for matching annotate_data.
annotate_labels	Logical, whether to label the annotated points.
zoom_on_annotations	Logical, whether to create a zoomed version of the plot focusing on annotated SNPs.
zoom_margin	Numeric, the margin size around zoomed points.
...	Additional arguments to be passed to ggplot2 plotting functions.

Value

An object of class 'ggplot' or 'plotly' depending on the 'interactive' parameter.

Examples

library(ggplot2)
library(plotly)
library(dplyr)
library(nortest)
library(ggforce)
library(reshape2)
library(gridExtra)
library(grid)
library(cowplot)
flex_qqplot(example_data1, user_colors = c("black", "darkorange"))
flex_qqplot(example_data1, display_ks = TRUE, interactive = FALSE)
annotated_snps <- c("SNP_1", "SNP_2", "SNP_3")
flex_qqplot(example_data1, annotate_data = annotated_snps, annotate_labels = TRUE)
flex_qqplot(example_data1, annotate_data = annotated_snps, annotate_labels = TRUE, 
display_ks = TRUE)
flex_qqplot(example_data1, annotate_data = annotated_snps, annotate_labels = TRUE, 
zoom_on_annotations = TRUE, zoom_margin = 0.3, user_plot_theme = theme_bw())

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