integrated seektopic, cite format, and improved readme

docs/functions/convertEmbeddingsToUMAP.html

@@ -30,17 +30,17 @@
 </li>
 </ol>
 <p><a href="https://pair-code.github.io/understanding-umap/" target="_blank" class="external">Understanding UMAP</a> <br>
-<a href="https://www.youtube.com/watch?v=VPq4Ktf2zJ4" target="_blank" class="external">UMAP Algorithm Overview</a> <br>
-<img src="https://i.imgur.com/JEO6fE1.png" width="350px">
-<img src="https://i.imgur.com/Wzat3qY.png" width="1000px"></p>
-</div><div class="tsd-parameters"><h4 class="tsd-parameters-title">Parameters</h4><ul class="tsd-parameter-list"><li><span><span class="tsd-kind-parameter">embeddingsDict</span>: <span class="tsd-signature-symbol">{}</span></span><div class="tsd-comment tsd-typography"><p>The dictionary of embeddings.</p>
+<a href="https://www.youtube.com/watch?v=VPq4Ktf2zJ4" target="_blank" class="external">UMAP Algorithm Overview</a> <br></p>
+<img src="https://i.imgur.com/Wzat3qY.png" width="1000px">
+<img src="https://github.com/QwkSearch/datamapplot/blob/main/examples/plot_simple_arxiv.png?raw=true" width="1000px">
+<img src="https://github.com/QwkSearch/datamapplot/raw/main/examples/ArXiv_example.gif" width="1000px"></div><div class="tsd-parameters"><h4 class="tsd-parameters-title">Parameters</h4><ul class="tsd-parameter-list"><li><span><span class="tsd-kind-parameter">embeddingsDict</span>: <span class="tsd-signature-symbol">{}</span></span><div class="tsd-comment tsd-typography"><p>The dictionary of embeddings.</p>
 </div><div class="tsd-comment tsd-typography"></div><ul class="tsd-parameters"></ul></li><li><span><code class="tsd-tag">Optional</code><span class="tsd-kind-parameter">options</span>: <span class="tsd-signature-symbol">{ </span><br/><span>    </span><span class="tsd-kind-property">numberDimensions</span><span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">number</span><span class="tsd-signature-symbol">; </span><br/><span>    </span><span class="tsd-kind-property">numberNeighbors</span><span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">number</span><span class="tsd-signature-symbol">; </span><br/><span>    </span><span class="tsd-kind-property">numberDistance</span><span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">number</span><span class="tsd-signature-symbol">; </span><br/><span class="tsd-signature-symbol">}</span><span class="tsd-signature-symbol"> = {}</span></span><div class="tsd-comment tsd-typography"></div><ul class="tsd-parameters"><li class="tsd-parameter"><h5><span class="tsd-kind-property">number<wbr/>Dimensions</span><span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">number</span></h5><div class="tsd-comment tsd-typography"><p>[default=2] - The number of dimensions for UMAP output.</p>
 </div><div class="tsd-comment tsd-typography"></div></li><li class="tsd-parameter"><h5><span class="tsd-kind-property">number<wbr/>Neighbors</span><span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">number</span></h5><div class="tsd-comment tsd-typography"><p>[default=15] - The number of nearest neighbors for UMAP.</p>
 </div><div class="tsd-comment tsd-typography"></div></li><li class="tsd-parameter"><h5><span class="tsd-kind-property">number<wbr/>Distance</span><span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">number</span></h5><div class="tsd-comment tsd-typography"><p>[default=0.1] - The minimum distance parameter for UMAP.</p>
 </div><div class="tsd-comment tsd-typography"></div></li></ul></li></ul></div><h4 class="tsd-returns-title">Returns <span class="tsd-signature-type">Promise</span><span class="tsd-signature-symbol">&lt;</span><span class="tsd-signature-type">PlotDataPoint</span><span class="tsd-signature-symbol">[]</span><span class="tsd-signature-symbol">&gt;</span></h4><p>An array of plot data points.</p>
 <div class="tsd-comment tsd-typography"><h4 class="tsd-anchor-link"><a id="Author" class="tsd-anchor"></a>Author<a href="#Author" aria-label="Permalink" class="tsd-anchor-icon"><svg viewBox="0 0 24 24"><use href="../assets/icons.svg#icon-anchor"></use></svg></a></h4><p><a href="https://arxiv.org/abs/1802.03426" target="_blank" class="external">McInnes et al. (2018)</a> <br />
 <a href="https://pair-code.github.io/understanding-umap/" target="_blank" class="external">Coenen et al. (2019)</a></p>
-</div><aside class="tsd-sources"><ul><li>Defined in <a href="https://github.com/vtempest/ai-research-agent/tree/master/src/similarity/embeddings-to-graph.js#L46">similarity/embeddings-to-graph.js:46</a></li></ul></aside></li></ul></section></div><div class="col-sidebar"><div class="page-menu"><div class="tsd-navigation settings"><details class="tsd-accordion"><summary class="tsd-accordion-summary"><h3><svg width="20" height="20" viewBox="0 0 24 24" fill="none"><use href="../assets/icons.svg#icon-chevronDown"></use></svg>Settings</h3></summary><div class="tsd-accordion-details"><div class="tsd-filter-visibility"><span class="settings-label">Member Visibility</span><ul id="tsd-filter-options"><li class="tsd-filter-item"><label class="tsd-filter-input"><input type="checkbox" id="tsd-filter-protected" name="protected"/><svg width="32" height="32" viewBox="0 0 32 32" aria-hidden="true"><rect class="tsd-checkbox-background" width="30" height="30" x="1" y="1" rx="6" fill="none"></rect><path class="tsd-checkbox-checkmark" d="M8.35422 16.8214L13.2143 21.75L24.6458 10.25" stroke="none" stroke-width="3.5" stroke-linejoin="round" fill="none"></path></svg><span>Protected</span></label></li><li class="tsd-filter-item"><label class="tsd-filter-input"><input type="checkbox" id="tsd-filter-inherited" name="inherited" checked/><svg width="32" height="32" viewBox="0 0 32 32" aria-hidden="true"><rect class="tsd-checkbox-background" width="30" height="30" x="1" y="1" rx="6" fill="none"></rect><path class="tsd-checkbox-checkmark" d="M8.35422 16.8214L13.2143 21.75L24.6458 10.25" stroke="none" stroke-width="3.5" stroke-linejoin="round" fill="none"></path></svg><span>Inherited</span></label></li><li class="tsd-filter-item"><label class="tsd-filter-input"><input type="checkbox" id="tsd-filter-external" name="external"/><svg width="32" height="32" viewBox="0 0 32 32" aria-hidden="true"><rect class="tsd-checkbox-background" width="30" height="30" x="1" y="1" rx="6" fill="none"></rect><path class="tsd-checkbox-checkmark" d="M8.35422 16.8214L13.2143 21.75L24.6458 10.25" stroke="none" stroke-width="3.5" stroke-linejoin="round" fill="none"></path></svg><span>External</span></label></li></ul></div><div class="tsd-theme-toggle"><label class="settings-label" for="tsd-theme">Theme</label><select id="tsd-theme"><option value="os">OS</option><option value="light">Light</option><option value="dark">Dark</option></select></div></div></details></div><details open class="tsd-accordion tsd-page-navigation"><summary class="tsd-accordion-summary"><h3><svg width="20" height="20" viewBox="0 0 24 24" fill="none"><use href="../assets/icons.svg#icon-chevronDown"></use></svg>On This Page</h3></summary><div class="tsd-accordion-details"><a href="#md:umap-convert-embeddings-to-2d-or-3d-graph"><span>UMAP: <wbr/>Convert <wbr/>Embeddings to 2<wbr/>D or 3<wbr/>D <wbr/>Graph</span></a></div></details></div><div class="site-menu"><nav id="tsd-sidebar-links" class="tsd-navigation"><a href="https://github.com/vtempest/ai-research-agent">Source Code</a><a href="https://qwksearch.com">Live Demo</a><a href="https://discord.gg/SJdBqBz3tV">Discord Chat</a><a href="https://github.com/vtempest/ai-research-agent" class="tsd-nav-link">Source Code</a><a href="https://qwksearch.com" class="tsd-nav-link">Live Demo</a><a href="https://discord.gg/SJdBqBz3tV" class="tsd-nav-link">Discord Chat</a></nav><nav class="tsd-navigation"><a href="../modules.html"><svg class="tsd-kind-icon" viewBox="0 0 24 24"><use href="../assets/icons.svg#icon-1"></use></svg><span>ai-research-agent</span></a><ul class="tsd-small-nested-navigation" id="tsd-nav-container" data-base=".."><li>Loading...</li></ul></nav></div></div></div><footer></footer><div class="overlay"></div><script async src="https://www.googletagmanager.com/gtag/js?id=G-E5TZ32BZDF"></script><script>window.dataLayer = window.dataLayer || [];
+</div><aside class="tsd-sources"><ul><li>Defined in <a href="https://github.com/vtempest/ai-research-agent/tree/master/src/similarity/embeddings-to-graph.js#L48">similarity/embeddings-to-graph.js:48</a></li></ul></aside></li></ul></section></div><div class="col-sidebar"><div class="page-menu"><div class="tsd-navigation settings"><details class="tsd-accordion"><summary class="tsd-accordion-summary"><h3><svg width="20" height="20" viewBox="0 0 24 24" fill="none"><use href="../assets/icons.svg#icon-chevronDown"></use></svg>Settings</h3></summary><div class="tsd-accordion-details"><div class="tsd-filter-visibility"><span class="settings-label">Member Visibility</span><ul id="tsd-filter-options"><li class="tsd-filter-item"><label class="tsd-filter-input"><input type="checkbox" id="tsd-filter-protected" name="protected"/><svg width="32" height="32" viewBox="0 0 32 32" aria-hidden="true"><rect class="tsd-checkbox-background" width="30" height="30" x="1" y="1" rx="6" fill="none"></rect><path class="tsd-checkbox-checkmark" d="M8.35422 16.8214L13.2143 21.75L24.6458 10.25" stroke="none" stroke-width="3.5" stroke-linejoin="round" fill="none"></path></svg><span>Protected</span></label></li><li class="tsd-filter-item"><label class="tsd-filter-input"><input type="checkbox" id="tsd-filter-inherited" name="inherited" checked/><svg width="32" height="32" viewBox="0 0 32 32" aria-hidden="true"><rect class="tsd-checkbox-background" width="30" height="30" x="1" y="1" rx="6" fill="none"></rect><path class="tsd-checkbox-checkmark" d="M8.35422 16.8214L13.2143 21.75L24.6458 10.25" stroke="none" stroke-width="3.5" stroke-linejoin="round" fill="none"></path></svg><span>Inherited</span></label></li><li class="tsd-filter-item"><label class="tsd-filter-input"><input type="checkbox" id="tsd-filter-external" name="external"/><svg width="32" height="32" viewBox="0 0 32 32" aria-hidden="true"><rect class="tsd-checkbox-background" width="30" height="30" x="1" y="1" rx="6" fill="none"></rect><path class="tsd-checkbox-checkmark" d="M8.35422 16.8214L13.2143 21.75L24.6458 10.25" stroke="none" stroke-width="3.5" stroke-linejoin="round" fill="none"></path></svg><span>External</span></label></li></ul></div><div class="tsd-theme-toggle"><label class="settings-label" for="tsd-theme">Theme</label><select id="tsd-theme"><option value="os">OS</option><option value="light">Light</option><option value="dark">Dark</option></select></div></div></details></div><details open class="tsd-accordion tsd-page-navigation"><summary class="tsd-accordion-summary"><h3><svg width="20" height="20" viewBox="0 0 24 24" fill="none"><use href="../assets/icons.svg#icon-chevronDown"></use></svg>On This Page</h3></summary><div class="tsd-accordion-details"><a href="#md:umap-convert-embeddings-to-2d-or-3d-graph"><span>UMAP: <wbr/>Convert <wbr/>Embeddings to 2<wbr/>D or 3<wbr/>D <wbr/>Graph</span></a></div></details></div><div class="site-menu"><nav id="tsd-sidebar-links" class="tsd-navigation"><a href="https://github.com/vtempest/ai-research-agent">Source Code</a><a href="https://qwksearch.com">Live Demo</a><a href="https://discord.gg/SJdBqBz3tV">Discord Chat</a><a href="https://github.com/vtempest/ai-research-agent" class="tsd-nav-link">Source Code</a><a href="https://qwksearch.com" class="tsd-nav-link">Live Demo</a><a href="https://discord.gg/SJdBqBz3tV" class="tsd-nav-link">Discord Chat</a></nav><nav class="tsd-navigation"><a href="../modules.html"><svg class="tsd-kind-icon" viewBox="0 0 24 24"><use href="../assets/icons.svg#icon-1"></use></svg><span>ai-research-agent</span></a><ul class="tsd-small-nested-navigation" id="tsd-nav-container" data-base=".."><li>Loading...</li></ul></nav></div></div></div><footer></footer><div class="overlay"></div><script async src="https://www.googletagmanager.com/gtag/js?id=G-E5TZ32BZDF"></script><script>window.dataLayer = window.dataLayer || [];
 function gtag(){dataLayer.push(arguments);}
 gtag('js', new Date());
 gtag('config', 'G-E5TZ32BZDF');</script></body></html>