EntroPlots

Sequence logo plots from position frequency matrices (PFMs) — for DNA, RNA, and protein motifs.

Documentation for EntroPlots.

using EntroPlots

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]

logoplot(pfm)

Installation

using Pkg; Pkg.add("EntroPlots")

Reading a logo

• x-axis — position in the motif.
• y-axis — information content in bits (entropy reduction relative to the background).
• letter height — frequency × information content.
• letter stacking — most frequent symbol on top.

The PFM (4 × N for DNA/RNA, 20 × N for protein, columns summing to 1) is the only required input.

Next steps

• Guide — a cookbook of common tasks: custom backgrounds, minimal styling, highlighting regions, protein and RNA motifs, and saving to file.
• API Reference — full documentation of every exported function.

Acknowledgments

Glyph data and the base recipe pattern are adapted from LogoPlots.jl.