EntroPlots.jl

A Julia package for creating sequence logo plots from position frequency matrices (PFMs). EntroPlots.jl visualizes DNA, RNA, and protein motifs with information-theoretic scaling, custom backgrounds, and flexible highlighting options.

Features

• DNA/RNA motifs: Standard 4-letter nucleotide logos
• Protein motifs: 20 amino acid sequence visualization
• Custom backgrounds: Non-uniform base/amino acid frequencies
• Region highlighting: Emphasize important motif positions
• Publication ready: Clean styling with PNG/SVG output
• Information content: Proper bits scaling based on entropy reduction

Installation

using Pkg
Pkg.add("EntroPlots")

Quick Start

using EntroPlots

# Position frequency matrix (each column sums to 1)
pfm = [0.02  1.0  0.98  0.0   0.0   0.0   0.98  0.0   0.18  1.0
       0.98  0.0  0.02  0.19  0.0   0.96  0.01  0.89  0.03  0.0
       0.0   0.0  0.0   0.77  0.01  0.0   0.0   0.0   0.56  0.0
       0.0   0.0  0.0   0.04  0.99  0.04  0.01  0.11  0.23  0.0]

# Create logo plot
logoplot(pfm)

Usage

Basic Plotting

# With custom background probabilities
background = [0.25, 0.25, 0.25, 0.25]  # A, C, G, T
logoplot(pfm, background)

# With uniform background (default)
logoplot(pfm)

# Minimal styling
logoplot(pfm; _margin_=0Plots.mm, tight=true, yaxis=false, xaxis=false)

Highlighting Regions

Emphasize specific positions in your motif:

highlighted_regions = [4:8]
logoplot_with_highlight(pfm, background, highlighted_regions)

Protein Motifs

For protein sequences (20 amino acids):

# Generate example protein data
matrix = rand(20, 25)
pfm_protein = matrix ./ sum(matrix, dims=1)
reduce_entropy!(pfm_protein)

# Plot protein logo
logoplot(pfm_protein; protein=true)

With highlighting:

logoplot_with_highlight(pfm_protein, [2:5, 8:12, 21:25]; protein=true)

Saving Plots

# Save DNA/RNA logos
save_logoplot(pfm, background, "logo.png")
save_logoplot(pfm, "logo.png")  # uses default background

# Save protein logos  
save_logoplot(pfm_protein, "protein_logo.png"; protein=true)
save_logoplot(pfm_protein, "protein_highlight.png"; 
              protein=true, highlighted_regions=[2:5, 8:12])

API Reference

The package provides a simple interface centered around these main functions:

• logoplot(pfm, background=nothing; kwargs...) - Create a logo plot
• logoplot_with_highlight(pfm, regions; kwargs...) - Plot with highlighted regions
• save_logoplot(pfm, filename; kwargs...) - Save plot to file
• reduce_entropy!(pfm) - Apply entropy reduction (useful for protein data)

Plot interpretation:

• X-axis: Position in the sequence motif
• Y-axis: Information content (bits)
• Letter height: Proportional to frequency × information content
• Letter stacking: Most frequent nucleotides/amino acids on top

Acknowledgments

This package builds upon and modifies code from LogoPlots.jl.