BioMakie.jl

This package provides plotting functions for protein structures, multiple sequence alignments, and some other related plots like protein structure contact maps.

So far, plotting methods exist for packages:

• BioStructures.jl
• MIToS.jl
• FastaIO.jl
• FASTX.jl

Plotting methods in development:

• MolecularGraph.jl
• ProtoSyn.jl

Installation

Enter the package mode by pressing ] and run add BioMakie.

Usage

The main plotting functions are plotstruc and plotmsa, along with their mutating versions, plotstruc! and plotmsa!. The mutating functions allow the user to add multiple plots to the same Figure, using grid positions.

using BioMakie
using GLMakie
using BioStructures
struc = retrievepdb("2vb1") |> Observable
## or
struc = read("2vb1.pdb", BioStructures.PDB) |> Observable

fig = Figure()
plotstruc!(fig, struc; plottype = :ballandstick, gridposition = (1,1), atomcolors = aquacolors)
plotstruc!(fig, struc; plottype = :covalent, gridposition = (1,2))

To view a multiple sequence alignment, use the plotmsa function with a Pfam MSA or fasta file.

using FASTX
reader = open(FASTX.FASTA.Reader, "PF00062_full.fasta")
msa = [reader...] |> Observable
close(reader)
## or 
using MIToS
using MIToS.MSA
msa = MIToS.MSA.read("pf00062.stockholm.gz", Stockholm)

fig = plotmsa(msa; colorscheme = :tableau_blue_green)

Additional examples

Alpha shapes can be used to visualize the surface of a protein structure