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Documenter.jl committed Oct 28, 2023
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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-28T23:10:21","documenter_version":"1.1.2"}}
{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-28T23:12:48","documenter_version":"1.1.2"}}
24 changes: 12 additions & 12 deletions dev/api/index.html

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2 changes: 1 addition & 1 deletion dev/examples/genes/index.html
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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/$(gene)-gene.png&quot;, f, px_per_unit = 4)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../summary/">« Munging summary statistics</a><a class="docs-footer-nextpage" href="../isoforms/">Plotting isoforms »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Saturday 28 October 2023 23:10">Saturday 28 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
f</code></pre><p><img src="../../figs/CACNA1G-gene-line.png" alt/></p><p>Then we can save the figure as below.</p><pre><code class="language-julia hljs">save(&quot;figs/$(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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Saturday 28 October 2023 23:12">Saturday 28 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/examples/gtf/index.html
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h = [&quot;seqnames&quot;, &quot;source&quot;, &quot;feature&quot;, &quot;start&quot;, &quot;end&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;phase&quot;, &quot;info&quot;]
gencode = CSV.read(&quot;data/gencode/$(file)&quot;, DataFrame; delim = &quot;\t&quot;, comment = &quot;#&quot;, header = h)</code></pre><div class="admonition is-warning"><header class="admonition-header">Human genome build</header><div class="admonition-body"><p>The latest human genome assembly is <a href="https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh38.p14">GRCh38</a>, but we use an annotation with coordinates from the older version (GRCh37), because a lot of the GWAS results are shared in GRCh37 genomic coordinates. Make sure to use the matching human genome build when visualizing your results. </p></div></div><p>The ninth column of a <a href="https://uswest.ensembl.org/info/website/upload/gff.html">GTF file</a> contains rich information about features, so we can parse this column.</p><pre><code class="language-julia hljs">GeneticsMakie.parsegtf!(gencode)</code></pre><div class="admonition is-info"><header class="admonition-header">Chromosome names</header><div class="admonition-body"><p>Chromosome names are munged to not contain “chr” prefix, and their type is <code>String</code>, since there could be non-numerical chromosome names, such as sex chromosomes and mitochondrial genome.</p></div></div><p>To reduce memory intake, we can also subset <code>gencode</code> to most commonly used columns in downstream analyses.</p><pre><code class="language-julia hljs">select!(gencode, :seqnames, :feature, :start, :end, :strand, :gene_id, :gene_name, :gene_type, :transcript_id)</code></pre><p>To further reduce memory intake, we can instead store and load GENCODE annotation as an Arrow file. </p><pre><code class="language-julia hljs">Arrow.write(&quot;data/gencode/$(splitext(file)[1]).arrow&quot;, gencode)
gencode = Arrow.Table(&quot;data/gencode/$(splitext(file)[1]).arrow&quot;)|&gt; DataFrame</code></pre><p>Other transcriptome annotations, such as one from RefSeq, can be used for plotting functions as long as they contain the above columns with the right column names.</p><p>Once <code>gencode</code> is ready, we can look up where a gene is on the human genome.</p><pre><code class="language-julia hljs">GeneticsMakie.findgene(&quot;RBFOX1&quot;, gencode)
GeneticsMakie.findgene(&quot;ENSG00000078328&quot;, gencode)</code></pre><div class="admonition is-success"><header class="admonition-header">Gene names</header><div class="admonition-body"><p>Make sure to use the correct gene name in case the gene cannot be found. The latest gene names can be looked up in databases such as <a href="https://www.genecards.org/">GeneCards</a>.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« Home</a><a class="docs-footer-nextpage" href="../summary/">Munging summary statistics »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Saturday 28 October 2023 23:10">Saturday 28 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
GeneticsMakie.findgene(&quot;ENSG00000078328&quot;, gencode)</code></pre><div class="admonition is-success"><header class="admonition-header">Gene names</header><div class="admonition-body"><p>Make sure to use the correct gene name in case the gene cannot be found. The latest gene names can be looked up in databases such as <a href="https://www.genecards.org/">GeneCards</a>.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« Home</a><a class="docs-footer-nextpage" href="../summary/">Munging summary statistics »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Saturday 28 October 2023 23:12">Saturday 28 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/examples/gwas/index.html
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rowgap!(f.layout, 1, 0)
rowgap!(f.layout, 2, 5)
resize_to_layout!(f)
f</code></pre><p><img src="../../figs/qq.png" alt/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../locus/">« Plotting LocusZoom</a><a class="docs-footer-nextpage" href="../twas/">Plotting TWAS »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Saturday 28 October 2023 23:10">Saturday 28 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
f</code></pre><p><img src="../../figs/qq.png" alt/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../locus/">« Plotting LocusZoom</a><a class="docs-footer-nextpage" href="../twas/">Plotting TWAS »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Saturday 28 October 2023 23:12">Saturday 28 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/examples/isoforms/index.html
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GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, range1, range2)
rowsize!(f.layout, 1, rs)
resize_to_layout!(f)
f</code></pre><p><img src="../../figs/GRIN2A-isoform-highlights.png" alt/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../genes/">« Plotting genes</a><a class="docs-footer-nextpage" href="../locus/">Plotting LocusZoom »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Saturday 28 October 2023 23:10">Saturday 28 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
f</code></pre><p><img src="../../figs/GRIN2A-isoform-highlights.png" alt/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../genes/">« Plotting genes</a><a class="docs-footer-nextpage" href="../locus/">Plotting LocusZoom »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Saturday 28 October 2023 23:12">Saturday 28 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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