HOMER Plotting Tools

A collection of R scripts for creating publication-quality visualizations from HOMER (Hypergeometric Optimization of Motif EnRichment) analysis outputs. This toolkit enhances HOMER's capabilities with customizable plotting functions for motif analysis, peak annotations, and genomic feature distributions.

Table of Contents

• Overview
• Features
• Installation
• Usage
• Plot Types
• Configuration
• Contributing

Overview

This toolkit extends HOMER's functionality by providing advanced visualization capabilities for:

• Motif enrichment analysis
• Peak distribution plots
• Genomic feature annotations
• Tag density heatmaps
• Integration with other NGS data

Features

• Publication-ready plot generation
• Customizable visualization parameters
• Multiple plot types and styles
• Batch processing capabilities
• Integration with HOMER outputs
• Statistical annotation options
• High-resolution export formats

Installation

1. Clone the repository:

git clone https://github.com/yourusername/rrjHomerPlots.git
cd rrjHomerPlots

2. Install R dependencies:

install.packages(c(
  "ggplot2",
  "ComplexHeatmap",
  "GenomicRanges",
  "rtracklayer",
  "gridExtra"
))

3. Ensure HOMER is installed and in your PATH

Usage

Basic Plotting

# Load the plotting library
source("homer_plots.R")

# Create motif enrichment plot
plot_motif_enrichment("path/to/homer/output", 
                     top_n = 10,
                     plot_type = "barplot")

# Generate peak distribution
plot_peak_distribution("path/to/peaks.txt",
                      genome = "hg19",
                      window_size = 2000)

Batch Processing

# Process multiple datasets
process_multiple_outputs(
  input_dir = "homer_results/",
  output_dir = "plots/",
  plot_types = c("motif", "distribution")
)

Plot Types

1. Motif Enrichment

• Bar plots of enrichment scores
• Logo plots for motif sequences
• P-value distribution plots
• Combined motif-score visualizations

2. Peak Distribution

• Genome-wide distribution plots
• Feature-centered heatmaps
• Distance to TSS plots
• Chromosome-wise distribution

3. Feature Annotation

• Genomic feature pie charts
• Feature enrichment plots
• Region overlap plots
• Custom annotation plots

4. Tag Density

• Profile plots
• Heatmaps
• Aggregation plots
• Multi-sample comparisons

Plot Customization

Color Schemes

# Default color palettes
homer_colors <- c(
  "primary" = "#4285F4",
  "secondary" = "#34A853",
  "accent" = "#EA4335"
)

# Custom theme settings
homer_theme <- theme_minimal() +
  theme(
    axis.text = element_text(size = 12),
    axis.title = element_text(size = 14, face = "bold")
  )

Layout Options

# Configure plot dimensions
plot_config <- list(
  width = 8,
  height = 6,
  dpi = 300,
  format = "pdf"
)

Data Requirements

Input Formats

1. HOMER output files
2. BED/narrowPeak files
3. Tag directories
4. Genome annotations

File Structure

project/
├── data/
│   ├── peaks/          # Peak files
│   ├── motifs/         # Motif analysis
│   └── tags/           # Tag directories
└── output/
    └── plots/          # Generated plots

Configuration

Global Settings

# Set global parameters
options(
  homer.genome = "hg19",
  homer.plot.width = 8,
  homer.plot.height = 6,
  homer.plot.dpi = 300
)

Plot-Specific Settings

# Motif plot settings
motif_params <- list(
  max_motifs = 10,
  p_cutoff = 0.05,
  sort_by = "p.value"
)

# Distribution plot settings
dist_params <- list(
  window = 2000,
  bin_size = 50,
  smooth = TRUE
)

Contributing

1. Fork the repository
2. Create your feature branch
3. Add your plotting functions
4. Submit a pull request

Development Guidelines

• Follow R style guidelines
• Document all functions
• Include example plots
• Add unit tests

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use these plotting tools in your research, please cite:

Author et al. (Year). HOMER Plotting Tools: Enhanced visualization for HOMER analysis.
Repository: https://github.com/yourusername/rrjHomerPlots

Related Projects

• HOMER
• ATACseq_Pipeline
• goronzy_lab

Acknowledgments

• HOMER development team
• R visualization packages
• Supporting institutions
• Bioinformatics community