Skill: Manhattan Plot (R)

Category

Omics

When to Use

Manhattan plot is a graph used to describe the relationship between mutations on chromosomes and traits. It is named Manhattan plot because it resembles the urban landscape of Manhattan, USA. Manhattan plot is generally drawn in the form of scatter plot, but it can also be displayed in bar chart or line chart. It is usually drawn using R package qqman or directly using ggplot2.

Required R Packages

• aplot
• qqman
• tidyverse

Minimal Reproducible Code

# Load packages
library(aplot)
library(qqman)
library(tidyverse)

# Prepare data
# View the dataset
head(gwasResults)

# Create visualization
# Basic manhattan plot
manhattan(gwasResults)

Key Parameters

• x: Maps BP to the x aesthetic
• alpha: Controls transparency (0 = fully transparent, 1 = opaque)
• position: Position adjustment (identity, dodge, stack, fill)
• theme: Plot theme; tutorial uses theme_bw()

Tips

• Use theme_minimal() or theme_bw() for clean, publication-ready plots
• Customize color scales with scale_fill_manual() or scale_color_brewer()
• Include appropriate statistical thresholds (e.g., FDR < 0.05, |log2FC| > 1) in the visualization

Full Tutorial

https://openbiox.github.io/Bizard/Omics/ManhattanPlot.html