https://github.com/biojulia/biomakie.jl

Plotting and interface tools for biology.
https://github.com/biojulia/biomakie.jl

Last synced: about 1 year ago
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Plotting and interface tools for biology.

• Host: GitHub
• URL: https://github.com/biojulia/biomakie.jl
• Owner: BioJulia
• License: mit
• Created: 2020-02-25T23:27:43.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2024-10-23T01:21:32.000Z (over 1 year ago)
• Last Synced: 2024-10-30T01:36:58.919Z (over 1 year ago)
• Language: Julia
• Homepage: https://biojulia.dev/BioMakie.jl/
• Size: 61.2 MB
• Stars: 56
• Watchers: 3
• Forks: 4
• Open Issues: 14
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          


## **Status:**

[![Latest release](https://img.shields.io/github/release/BioJulia/BioMakie.jl.svg)](https://github.com/BioJulia/BioMakie.jl/releases/latest)

[![License](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/BioMakie.jl/blob/master/LICENSE.md)

[![ci](https://github.com/BioJulia/BioMakie.jl/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/BioJulia/BioMakie.jl/actions/workflows/ci.yml)

## **Documentation:**

[![Docs](https://img.shields.io/badge/docs-dev-blue.svg?label=documentation)](https://BioJulia.github.io/BioMakie.jl/dev)

## Installation

To install BioMakie, access the Julia package manager by

pressing **`]`** from the Julia REPL, then run **`add BioMakie`**.

## Contributing and questions

Anyone can contribute to this package, by doing things like reporting bugs, fixing issues,

improving performance, adding new features, and adding examples. Feel free to open an **Issue** or **Pull Request**,

or communicate on the **#biology** or **#makie** channels of the [Julia Slack](https://join.slack.com/t/julialang/shared_invite/zt-1ab2rnvlw-mfODD9DJC_apVEULyKXDrA).

## About

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

It also provides more complicated examples that show off additional functionality and interfaces. 

The main plotting functions are **plotstruc** and **plotmsa**, along with their mutating versions, **plotstruc!** and **plotmsa!**.

```julia

using BioMakie

using GLMakie

using BioStructures

struc = retrievepdb("2vb1") |> Observable

## or

struc = read("2vb1.pdb", BioStructures.PDBFormat) |> 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.

```julia

using FASTX

reader = open(FASTX.FASTA.Reader, "PF00062_full.fasta")

msa = [reader...] |> Observable

close(reader)

## or 

using MIToS.MSA

msa = read_file("pf00062.stockholm.gz", Stockholm)

fig = plotmsa(msa; colorscheme = :tableau_blue_green)

```



## Other examples

### Viewing the frequencies of amino acids in a multiple sequence alignment



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



### Database information can be displayed for a protein (including a GPT response, OpenAI.jl)



### Protein residue mutation and changing rotamers (with ProtoSyn.jl)