make_mahattan script

This repository contains the script that I use to generate manhattan plots and to generate qqplots. This script is larger designed to work with REGENIE at the moment but hopefully will support more programs as time goes on.

Installation

To run this script, you need to have R installed along with the following R packages:

• optparse
• data.table
• ggplot2
• tidyverse
• ggrepel
• dplyr

You can install these dependencies by running the following command in your R console:

install.packages(c("optparse", "data.table", "tidyverse", "ggrepel"))

Note: dplyr and ggplot2 are included in tidyverse.

Alternatively, you can use the provided environment.yml file to create a Conda environment named "manhatten_env" with all dependencies installed:

# Using conda
conda env create -f environment.yml
conda activate manhattan_env

# Or using mamba (recommended for speed)
mamba env create -f environment.yml
mamba activate manhattan_env

Usage

The script is run from the command line using Rscript.

Input Data Requirements

The input data (single file) should contain the following columns:

• CHROM: Chromosome number (e.g., "1", "chr1")
• GENPOS: Genomic position
• A1FREQ: Allele frequency
• A p-value column (name specified by --pval-col, default is "PVal")

Example Command

Here is an example of how to run the script for a single GWAS result file:

Rscript make_manhattan.r \
  --input "path/to/gwas_results.txt" \
  --pheno-name "TraitName" \
  --output-dir "output_plots" \
  --pval-col "P_VALUE" \
  --maf-threshold 0.01 \
  --color-list "grey,skyblue"

Arguments

• --input: Path to the GWAS results file or directory.
• --pheno-name: Name of the phenotype (used for plot titles and filenames).
• --output-dir: Directory where the output plots will be saved.
• --pval-col: Name of the column containing p-values (default: "PVal").
• --maf-threshold: Minor Allele Frequency threshold for filtering (default: 0.01).
• --bonferroni: Bonferroni significance threshold (default: 5e-8).
• --suggestive: Suggestive significance threshold (default: 1e-5).
• --pattern: (Optional) File pattern to match if input is a directory.
• --x-axis-text-size: Size of the x-axis title text (default: 12).
• --y-axis-text-size: Size of the y-axis title text (default: 12).
• --title-text-size: Size of the plot title text (default: 14).
• --color-list: List of colors for the Manhattan plot, provided as a comma-separated string (default: "grey,skyblue").