build based on 426f5ff

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-04T23:14:11","documenter_version":"1.4.1"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-05T00:28:33","documenter_version":"1.4.1"}}

dev/examples/genes/index.html

@@ -60,4 +60,4 @@
 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/$(gene)-gene.png&quot;, f, px_per_unit = 4)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../summary/">« Munging summary statistics</a><a class="docs-footer-nextpage" href="../isoforms/">Plotting isoforms »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Tuesday 4 June 2024 23:14">Tuesday 4 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+f</code></pre><p><img src="../../figs/CACNA1G-gene-line.png" alt/></p><p>Then we can save the figure as below.</p><pre><code class="language-julia hljs">save(&quot;figs/$(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="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>

dev/examples/gtf/index.html

@@ -9,4 +9,4 @@
 h = ["seqnames", "source", "feature", "start", "end", "score", "strand", "phase", "info"]
 gencode = CSV.read(&quot;data/gencode/$(file)&quot;, DataFrame; delim = &quot;\t&quot;, comment = &quot;#&quot;, header = h)</code></pre><div class="admonition is-warning"><header class="admonition-header">Human genome build</header><div class="admonition-body"><p>The latest human genome assembly is <a href="https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh38.p14">GRCh38</a>, but we use an annotation with coordinates  from the older version (GRCh37), because a lot of the GWAS results are shared in  GRCh37 genomic coordinates. Make sure to use the matching human genome build when visualizing your results. </p></div></div><p>The ninth column of a <a href="https://www.gencodegenes.org/pages/data_format.html">GTF file</a>  contains rich information about features, so we can parse this column.</p><pre><code class="language-julia hljs">GeneticsMakie.parsegtf!(gencode)</code></pre><div class="admonition is-info"><header class="admonition-header">Chromosome names</header><div class="admonition-body"><p>Chromosome names are munged to not contain “chr” prefix, and their type is <code>String</code>, since there could be non-numerical chromosome names, such as sex chromosomes and mitochondrial genome.</p></div></div><p>To reduce memory intake, we can also subset <code>gencode</code> to most commonly used columns in downstream analyses.</p><pre><code class="language-julia hljs">select!(gencode, :seqnames, :feature, :start, :end, :strand, :gene_id, :gene_name, :gene_type, :transcript_id)</code></pre><p>To further reduce memory intake, we can instead store and load GENCODE annotation as an Arrow file. </p><pre><code class="language-julia hljs">Arrow.write(&quot;data/gencode/$(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="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 4 June 2024 23:14">Tuesday 4 June 2024</span>. Using Julia version 1.10.4.</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="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>

dev/examples/gwas/index.html

@@ -59,4 +59,4 @@
 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="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 4 June 2024 23:14">Tuesday 4 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/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="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>

dev/examples/isoforms/index.html

@@ -40,4 +40,4 @@
 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="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 4 June 2024 23:14">Tuesday 4 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/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="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>