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Documenter.jl committed Jun 11, 2024
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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-05T00:28:33","documenter_version":"1.4.1"}}
{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-11T22:55:39","documenter_version":"1.4.1"}}
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4 changes: 2 additions & 2 deletions dev/examples/genes/index.html
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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Plotting genes · GeneticsMakie.jl</title><meta name="title" content="Plotting genes · GeneticsMakie.jl"/><meta property="og:title" content="Plotting genes · GeneticsMakie.jl"/><meta property="twitter:title" content="Plotting genes · GeneticsMakie.jl"/><meta name="description" content="Documentation for GeneticsMakie.jl."/><meta property="og:description" content="Documentation for GeneticsMakie.jl."/><meta property="twitter:description" content="Documentation for GeneticsMakie.jl."/><meta property="og:url" content="https://mmkim1210.github.io/GeneticsMakie.jl/examples/genes/"/><meta property="twitter:url" content="https://mmkim1210.github.io/GeneticsMakie.jl/examples/genes/"/><link rel="canonical" href="https://mmkim1210.github.io/GeneticsMakie.jl/examples/genes/"/><script data-outdated-warner src="../../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="../.."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../../assets/documenter.js"></script><script src="../../search_index.js"></script><script src="../../siteinfo.js"></script><script src="../../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../../"><img src="../../assets/logo.svg" alt="GeneticsMakie.jl logo"/></a><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../../">Home</a></li><li><span class="tocitem">Examples</span><ul><li><a class="tocitem" href="../gtf/">Parsing GENCODE</a></li><li><a class="tocitem" href="../summary/">Munging summary statistics</a></li><li class="is-active"><a class="tocitem" href>Plotting genes</a></li><li><a class="tocitem" href="../isoforms/">Plotting isoforms</a></li><li><a class="tocitem" href="../locus/">Plotting LocusZoom</a></li><li><a class="tocitem" href="../gwas/">Plotting GWAS</a></li><li><a class="tocitem" href="../twas/">Plotting TWAS</a></li><li><a class="tocitem" href="../loops/">Plotting loops</a></li><li><a class="tocitem" href="../peaks/">Plotting peaks</a></li></ul></li><li><a class="tocitem" href="../../api/">API</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Examples</a></li><li class="is-active"><a href>Plotting genes</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Plotting genes</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/mmkim1210/GeneticsMakie.jl/blob/master/docs/src/examples/genes.md#" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Plotting-genes"><a class="docs-heading-anchor" href="#Plotting-genes">Plotting genes</a><a id="Plotting-genes-1"></a><a class="docs-heading-anchor-permalink" href="#Plotting-genes" title="Permalink"></a></h1><p>After <a href="../gtf/#Parsing-GENCODE">Parsing GENCODE</a>, we can start plotting gene bodies. <a href="https://github.com/mmkim1210/GeneticsMakie.jl"><strong>GeneticsMakie.jl</strong></a> is transparent in that it shows all genes within a genomic window.</p><pre><code class="language-julia hljs">using Pkg
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Plotting genes · GeneticsMakie</title><meta name="title" content="Plotting genes · GeneticsMakie"/><meta property="og:title" content="Plotting genes · GeneticsMakie"/><meta property="twitter:title" content="Plotting genes · GeneticsMakie"/><meta name="description" content="Documentation for GeneticsMakie."/><meta property="og:description" content="Documentation for GeneticsMakie."/><meta property="twitter:description" content="Documentation for GeneticsMakie."/><meta property="og:url" content="https://mmkim1210.github.io/GeneticsMakie.jl/examples/genes/"/><meta property="twitter:url" content="https://mmkim1210.github.io/GeneticsMakie.jl/examples/genes/"/><link rel="canonical" href="https://mmkim1210.github.io/GeneticsMakie.jl/examples/genes/"/><script data-outdated-warner src="../../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="../.."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../../assets/documenter.js"></script><script src="../../search_index.js"></script><script src="../../siteinfo.js"></script><script src="../../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../../"><img src="../../assets/logo.svg" alt="GeneticsMakie logo"/></a><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../../">Home</a></li><li><span class="tocitem">Examples</span><ul><li><a class="tocitem" href="../gtf/">Parsing GENCODE</a></li><li><a class="tocitem" href="../summary/">Munging summary statistics</a></li><li class="is-active"><a class="tocitem" href>Plotting genes</a></li><li><a class="tocitem" href="../isoforms/">Plotting isoforms</a></li><li><a class="tocitem" href="../locus/">Plotting LocusZoom</a></li><li><a class="tocitem" href="../gwas/">Plotting GWAS</a></li><li><a class="tocitem" href="../twas/">Plotting TWAS</a></li><li><a class="tocitem" href="../loops/">Plotting loops</a></li><li><a class="tocitem" href="../peaks/">Plotting peaks</a></li></ul></li><li><a class="tocitem" href="../../api/">API</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Examples</a></li><li class="is-active"><a href>Plotting genes</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Plotting genes</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/mmkim1210/GeneticsMakie.jl/blob/master/docs/src/examples/genes.md#" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Plotting-genes"><a class="docs-heading-anchor" href="#Plotting-genes">Plotting genes</a><a id="Plotting-genes-1"></a><a class="docs-heading-anchor-permalink" href="#Plotting-genes" title="Permalink"></a></h1><p>After <a href="../gtf/#Parsing-GENCODE">Parsing GENCODE</a>, we can start plotting gene bodies. <a href="https://github.com/mmkim1210/GeneticsMakie.jl"><strong>GeneticsMakie.jl</strong></a> is transparent in that it shows all genes within a genomic window.</p><pre><code class="language-julia hljs">using Pkg
Pkg.add([&quot;GeneticsMakie&quot;, &quot;CairoMakie&quot;, &quot;DataFrames&quot;, &quot;Arrow&quot;])

using GeneticsMakie, CairoMakie, DataFrames, Arrow
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resize_to_layout!(f)
vlines!(ax, start, color = (:gold, 0.5), linewidth = 0.5)
vlines!(ax, stop, color = (:gold, 0.5), linewidth = 0.5)
f</code></pre><p><img src="../../figs/CACNA1G-gene-line.png" alt/></p><p>Then we can save the figure as below.</p><pre><code class="language-julia hljs">save(&quot;figs/$(gene)-gene.png&quot;, f, px_per_unit = 4)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../summary/">« Munging summary statistics</a><a class="docs-footer-nextpage" href="../isoforms/">Plotting isoforms »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Wednesday 5 June 2024 00:28">Wednesday 5 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
f</code></pre><p><img src="../../figs/CACNA1G-gene-line.png" alt/></p><p>Then we can save the figure as below.</p><pre><code class="language-julia hljs">save(&quot;figs/$(gene)-gene.png&quot;, f, px_per_unit = 4)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../summary/">« Munging summary statistics</a><a class="docs-footer-nextpage" href="../isoforms/">Plotting isoforms »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Tuesday 11 June 2024 22:55">Tuesday 11 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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