flex_manhattan: flex_manhattan function

In GPflexViz: Graphical Visualizations Related to Genomic Prediction

flex_manhattan function

Description

This function creates a flexible Manhattan plot, which is useful for visualizing GWAS results. The plot can be generated as either a static or an interactive plot. The function allows customization of color schemes, titles, axis labels, and annotation features.

Usage

flex_manhattan(
  gwas_data,
  interactive = TRUE,
  user_colors = NULL,
  user_y_cutoff = -log10(5e-08),
  user_y_cutoff_color = "red",
  user_title = "Manhattan Plot",
  user_x_title = "Position",
  user_y_title = "-log10(p-value)",
  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)),
  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; if TRUE, returns an interactive plotly plot, otherwise a ggplot2 plot.
user_colors	A vector of colors for the chromosomes. If NULL, a default set of 22 colors is used.
user_y_cutoff	A numeric value for the y-axis cutoff, used to draw a horizontal line.
user_y_cutoff_color	Color of the y-axis cutoff line.
user_title	The main title of the plot.
user_x_title	The label for the x-axis.
user_y_title	The label for the y-axis.
user_legend_title	The title for the legend. If NULL, no legend is displayed.
user_plot_theme	ggplot2 theme object for styling the plot background and fonts.
user_plot_theme_specs	Additional ggplot2 theme specifications for custom styling.
annotate_data	A vector of SNP identifiers for which annotations are to be made.
annotate_column	The column name from gwas_data used for matching annotate_data.
annotate_labels	Logical; if TRUE, annotations are added to the plot.
zoom_on_annotations	Logical; if TRUE, the plot will zoom in on annotated SNPs.
zoom_margin	Numeric; defines the margin around the zoomed area as a proportion of the range of the data.
...	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_manhattan(example_data1)

# Changing the y-axis cutoff to highlight significant p-values differently
flex_manhattan(example_data1, 
               user_y_cutoff = c(5, 4),  # Multiple cutoffs
               user_y_cutoff_color = c("darkred", "darkgreen"))  # Corresponding colors

# Adding annotations for specific SNPs
annotated_snps <- c("SNP_2550", "SNP_4829", "SNP_8296")
flex_manhattan(example_data1, annotate_data = annotated_snps, annotate_labels = TRUE, 
interactive = FALSE)


# Example of placing the legend at the bottom with a black outline
flex_manhattan(example_data1, 
               user_plot_theme_specs = theme(
                 legend.position = "bottom",
                 legend.box.background = element_rect(colour = "black")
               ))
               

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