EntroPlots.jl

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

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)

Install

using Pkg; Pkg.add("EntroPlots")

Reading a logo

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

Cookbook

The PFM pfm (4 × N for DNA/RNA, 20 × N for protein, columns sum to 1) is the only required input. Every example below assumes using EntroPlots and reuses the pfm from above.

Custom background frequencies

logoplot(pfm, [0.3, 0.2, 0.2, 0.3])  # A, C, G, T

Minimal styling (no margins, no axes)

using Plots  # for `Plots.mm`
logoplot(pfm; _margin_=0Plots.mm, tight=true, yaxis=false, xaxis=false)

Highlight regions of interest

logoplot_with_highlight(pfm, [4:8])

Tight variant:

using Plots
logoplot_with_highlight(pfm, [4:8]; _margin_=0Plots.mm, tight=true)

Protein motifs (20 amino acids)

matrix = rand(20, 25)
pfm_protein = matrix ./ sum(matrix, dims=1)
reduce_entropy!(pfm_protein)  # sharpen toward dominant residue per column

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

RNA motifs

logoplot(pfm; rna=true)  # uses A, C, G, U

Saving to file

save_logoplot(pfm, "logo.png")                          # default uniform background
save_logoplot(pfm, [0.3, 0.2, 0.2, 0.3], "logo.png")    # custom background
save_logoplot(pfm_protein, "protein.png"; protein=true)
save_logoplot(pfm, "highlighted.png"; highlighted_regions=[4:8])

API

Function	Purpose
logoplot(pfm[, background]; kwargs...)	Render a logo plot.
logoplot_with_highlight(pfm[, background], regions; kwargs...)	Render with selected positions highlighted.
save_logoplot(pfm[, background], path; kwargs...)	Save to file (PNG / SVG / etc., inferred from extension).
reduce_entropy!(pfm; factor=10)	Sharpen each column toward its dominant residue. Useful for noisy protein PFMs.

Common keyword arguments: protein, rna, tight, _margin_, xaxis, yaxis, dpi, alpha, beta, uniform_color, pos, xrotation, scale_by_frequency.

Acknowledgments

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