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2 changes: 1 addition & 1 deletion README.html
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],
</code></pre><p>themeConfig: {</p></div></div></main><footer class="VPDocFooter" data-v-39a288b8 data-v-09de1c0f><!--[--><!--]--><!----><!----></footer><!--[--><!--]--></div></div></div><!--[--><!--]--></div></div><footer class="VPFooter" data-v-5d98c3a5 data-v-e315a0ad><div class="container" data-v-e315a0ad><p class="message" data-v-e315a0ad>Copyright © 2024-present Will Hannon and Jesse Bloom</p><!----></div></footer><!--[--><!--]--></div></div>
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2 changes: 1 addition & 1 deletion antibody_escape.html
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<div id="app"><div class="Layout" data-v-5d98c3a5><!--[--><!--]--><!--[--><span tabindex="-1" data-v-0f60ec36></span><a href="#VPContent" class="VPSkipLink visually-hidden" data-v-0f60ec36> Skip to content </a><!--]--><!----><header class="VPNav" data-v-5d98c3a5 data-v-ae24b3ad><div class="VPNavBar top" data-v-ae24b3ad data-v-ccf7ddec><div class="wrapper" data-v-ccf7ddec><div class="container" data-v-ccf7ddec><div class="title" data-v-ccf7ddec><div class="VPNavBarTitle" data-v-ccf7ddec data-v-ab179fa1><a class="title" href="/dms-vep-pipeline-3/" data-v-ab179fa1><!--[--><!--]--><!----><span data-v-ab179fa1>Homepage for `dms-vep-pipeline-3` test example</span><!--[--><!--]--></a></div></div><div class="content" data-v-ccf7ddec><div class="content-body" data-v-ccf7ddec><!--[--><!--]--><div class="VPNavBarSearch search" data-v-ccf7ddec><!----></div><nav aria-labelledby="main-nav-aria-label" class="VPNavBarMenu menu" data-v-ccf7ddec data-v-7f418b0f><span id="main-nav-aria-label" 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data-v-e5dd9c1c></span></span></button></div></div></div></div><div class="divider" data-v-ccf7ddec><div class="divider-line" data-v-ccf7ddec></div></div></div><!----></header><div class="VPLocalNav empty fixed" data-v-5d98c3a5 data-v-a6f0e41e><div class="container" data-v-a6f0e41e><!----><div class="VPLocalNavOutlineDropdown" style="--vp-vh:0px;" data-v-a6f0e41e data-v-267dd0ed><button data-v-267dd0ed>Return to top</button><!----></div></div></div><!----><div class="VPContent" id="VPContent" data-v-5d98c3a5 data-v-1428d186><div class="VPDoc" data-v-1428d186 data-v-39a288b8><!--[--><!--]--><div class="container" data-v-39a288b8><!----><div class="content" data-v-39a288b8><div class="content-container" data-v-39a288b8><!--[--><!--]--><main class="main" data-v-39a288b8><div style="position:relative;" class="vp-doc _dms-vep-pipeline-3_antibody_escape" data-v-39a288b8><div><h1 id="antibody-escape" tabindex="-1">Antibody Escape <a class="header-anchor" href="#antibody-escape" aria-label="Permalink to &quot;Antibody Escape&quot;">​</a></h1><p>Here&#39;s what a page with antibody escape data might look like.</p><h2 id="individual-antibody-selections" tabindex="-1">Individual Antibody Selections <a class="header-anchor" href="#individual-antibody-selections" aria-label="Permalink to &quot;Individual Antibody Selections&quot;">​</a></h2><p>You can include links to the antibody escape data created automatically by the <a href="https://github.com/dms-vep/dms-vep-pipeline-3" target="_blank" rel="noreferrer"><code>dms-vep-pipeline</code></a>.</p><ul><li><a href="./notebooks/fit_escape_antibody_escape_LibA-220210-REGN10933-1.html" target="_self">LibA-220210-REGN10933-1</a></li><li><a href="./notebooks/fit_escape_antibody_escape_LibA-220210-REGN10933-2.html" target="_self">LibA-220210-REGN10933-2</a></li><li><a href="./notebooks/fit_escape_antibody_escape_LibB-220302-REGN10933-1.html" target="_self">LibB-220302-REGN10933-1</a></li><li><a href="./notebooks/fit_escape_antibody_escape_LibA-220302-S2M11-1.html" target="_self">LibA-220302-S2M11-1</a></li><li><a href="./notebooks/fit_escape_antibody_escape_LibA-220302-S2M11-2.html" target="_self">LibA-220302-S2M11-2</a></li></ul><p>You do this using normal markdown syntax with one exception – you include <code>{target=&quot;_self&quot;}</code> after the link:</p><div class="language-bash vp-adaptive-theme"><button title="Copy Code" class="copy"></button><span class="lang">bash</span><pre class="shiki shiki-themes github-light github-dark vp-code"><code><span class="line"><span style="--shiki-light:#6F42C1;--shiki-dark:#B392F0;">-</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;"> [LibA-220210-REGN10933-1](</span><span style="--shiki-light:#6F42C1;--shiki-dark:#B392F0;">notebooks/fit_escape_antibody_escape_LibA-220210-REGN10933-1.html</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">){target</span><span style="--shiki-light:#D73A49;--shiki-dark:#F97583;">=</span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;">&quot;_self&quot;}</span></span></code></pre></div><p>This approach will work for any file that&#39;s ordinarily present in the <code>docs/</code> directory created by the pipeline. For example, <code>.html</code> files that contain <code>Altair</code> plots.</p><ul><li><a href="./htmls/REGN10933_mut_effect.html" target="_self">REGN10933 Escape</a></li><li><a href="./htmls/S2M11_mut_effect.html" target="_self">S2M11 Escape</a></li></ul><p>If you prefer, you can include <code>Altair</code> plots directly on the page.</p><figure data-v-63b12ce1><!--[--><div class="vega-chart-container"><div></div><button class="expand-btn"><i class="bi bi-arrows-angle-expand"></i></button></div><!--]--><figcaption data-v-63b12ce1>Effects of mutations on antibody neutralization by REGN10933</figcaption></figure><p>You do this using a custom html-like syntax.</p><div class="language-bash vp-adaptive-theme"><button title="Copy Code" class="copy"></button><span class="lang">bash</span><pre class="shiki shiki-themes github-light github-dark vp-code"><code><span class="line"><span style="--shiki-light:#D73A49;--shiki-dark:#F97583;">&lt;</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">Figure caption=</span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;">&quot;Effects of mutations on antibody neutralization by REGN10933&quot;</span><span style="--shiki-light:#D73A49;--shiki-dark:#F97583;">&gt;</span></span>
<span class="line"><span style="--shiki-light:#D73A49;--shiki-dark:#F97583;"> &lt;</span><span style="--shiki-light:#6F42C1;--shiki-dark:#B392F0;">Altair</span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;"> :showShadow=&quot;true&quot;</span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;"> :spec-url=&quot;&#39;htmls/REGN10933_mut_effect.html&#39;&quot;</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">&gt;&lt;</span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;">/Altai</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">r</span><span style="--shiki-light:#D73A49;--shiki-dark:#F97583;">&gt;</span></span>
<span class="line"><span style="--shiki-light:#D73A49;--shiki-dark:#F97583;">&lt;</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">/Figure</span><span style="--shiki-light:#D73A49;--shiki-dark:#F97583;">&gt;</span></span></code></pre></div><p>The code above creates the <code>Altair</code> plot using the <code>&lt;Altair&gt;&lt;/Altair&gt;</code> tag and adds a figure caption with the surrounding <code>&lt;Figure&gt;&lt;/Figure&gt;</code> tag.</p></div></div></main><footer class="VPDocFooter" data-v-39a288b8 data-v-09de1c0f><!--[--><!--]--><!----><!----></footer><!--[--><!--]--></div></div></div><!--[--><!--]--></div></div><footer class="VPFooter" data-v-5d98c3a5 data-v-e315a0ad><div class="container" data-v-e315a0ad><p class="message" data-v-e315a0ad>Copyright © 2024-present Will Hannon and Jesse Bloom</p><!----></div></footer><!--[--><!--]--></div></div>
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