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🧬High-performance genetics- and genomics-related data visualization using Makie.jl

Home Page: https://mmkim1210.github.io/GeneticsMakie.jl/dev/

License: MIT License

Julia 100.00%
genetics genomics julia visualization makie bioinformatics cairomakie gwas phewas locuszoom colocalization fine-mapping qtl linkage julia-language data-science multi-ethnic v2f multivariate openmendel

geneticsmakie.jl's Introduction

GeneticsMakie

Dev Build Status Coverage Downloads

Installation

GeneticsMakie.jl supports Julia v1.6 or later.

julia> ]
pkg> add GeneticsMakie

Documentation

Dev

Examples

Visualize 1 Mb window around KMT2E gene:

Highlight KMT2E gene and several nearby genes:

Visualize KMT2E isoforms:

Visualize KMT2E and nearby isoforms simultaneously:

Visualize KMT2E isoforms w/ randomly generated expression

Visualize LD for KMT2E locus:

Visualize LD as a square for KMT2E locus:

Visualize GWAS results for KMT2E locus:

Visualize GWAS results for KMT2E locus with the same reference SNPs for LD:

Visualize Manhattan plot:

Visualize Miami/Hudson plot:

Visualize QQ plot of P values:

Further examples

Patterns of association and LD:

Colocalization of GWAS signals:

Association results across multiple phenotypes:

MHC association for schizophrenia with increasing sample size:

LD structure for ~66,000 SNPs in MHC region:

References

Kim et al., (2022). GeneticsMakie.jl: A versatile and scalable toolkit for visualizing locus-level genetic and genomic data. Bioinformatics, https://doi.org/10.1093/bioinformatics/btac786.

geneticsmakie.jl's People

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Forkers

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geneticsmakie.jl's Issues

TagBot trigger issue

This issue is used to trigger TagBot; feel free to unsubscribe.

If you haven't already, you should update your TagBot.yml to include issue comment triggers.
Please see this post on Discourse for instructions and more details.

If you'd like for me to do this for you, comment TagBot fix on this issue.
I'll open a PR within a few hours, please be patient!

Example code for "Further examples"

Thanks for this wonderful pkg,

I would like to use GeneticsMakie to draw some gwas results similar to those in the "Patterns of association and LD" example in the README.md:
effect-LD

However, I have no idea how to start after reading the doc.

Could you please provide the example code for this example?

Thanks a lot!

All the best,

SongtaoGui

pre-computed LD

Hello and thanks for developing a great tool.
Is it possible to color SNPs by LD using pre-computed data of the format (variant1, variant2, r2)

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