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Please refer to the updated function, Palantir.RunDM, for the latest features and improvements.
This older version, in addition to calculating the diffusion map (dm) and multiscale_space (ms),
also calculates t-SNE. To use the t-SNE feature, the multicore-tsne package needs to be installed in the conda environment."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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    <h1>(Deprecated) Run Palantir Diffusion Map</h1>
    
    <div class="hidden name"><code>RunPalantirDiffusionMap.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This is a deprecated version of the Palantir Diffusion Map function.
Please refer to the updated function, <code><a href="Palantir-Methods.html">Palantir.RunDM</a></code>, for the latest features and improvements.
This older version, in addition to calculating the diffusion map (dm) and multiscale_space (ms),
also calculates t-SNE. To use the t-SNE feature, the <code>multicore-tsne</code> package needs to be installed in the conda environment.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">RunPalantirDiffusionMap</span><span class="op">(</span><span class="va">seu</span>, reduction <span class="op">=</span> <span class="st">"pca"</span>, n_components <span class="op">=</span> <span class="fl">20</span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>seu</dt>
<dd><p>A Seurat object.</p></dd>


<dt>reduction</dt>
<dd><p>A character string specifying the dimension reduction to use. Default: 'pca'.</p></dd>


<dt>n_components</dt>
<dd><p>An integer specifying how many dimensions to use as input. Default: 20.</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>A Seurat object with added dm, ms, and t-SNE embeddings.</p>
    </div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p><code><a href="Palantir-Methods.html">Palantir.RunDM</a></code> for the updated version of this function.</p></div>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://satijalab.org/seurat" class="external-link">Seurat</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">SeuratExtend</span><span class="op">)</span></span>
<span><span class="va">pbmc</span> <span class="op">&lt;-</span> <span class="fu">RunPalantirDiffusionMap</span><span class="op">(</span><span class="va">pbmc</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://satijalab.org/seurat/reference/DimPlot.html" class="external-link">DimPlot</a></span><span class="op">(</span><span class="va">pbmc</span>, reduction <span class="op">=</span> <span class="st">"tsne"</span>, label <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="op">}</span></span></code></pre></div>
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