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    <h1>Visualize Gene Expression Dynamics Along Trajectories with Heatmaps</h1>
    
    <div class="hidden name"><code>GeneTrendHeatmap-Methods.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function suite provides tools for visualizing gene expression dynamics along pseudotime trajectories using heatmaps, leveraging results from either Palantir or Slingshot pseudotime analyses. GeneTrendHeatmap.Palantir() and GeneTrendHeatmap.Slingshot() each cater to the specific formatting and requirements of the pseudotime data generated by their respective tools.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">GeneTrendHeatmap.Palantir</span><span class="op">(</span></span>
<span>  <span class="va">seu</span>,</span>
<span>  <span class="va">features</span>,</span>
<span>  pseudotime.data <span class="op">=</span> <span class="st">"Pseudotime"</span>,</span>
<span>  <span class="va">lineage</span>,</span>
<span>  magic <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  scale <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  sort <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  color_scheme <span class="op">=</span> <span class="st">"D"</span>,</span>
<span>  conda_env <span class="op">=</span> <span class="st">"seuratextend"</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">GeneTrendHeatmap.Slingshot</span><span class="op">(</span></span>
<span>  <span class="va">seu</span>,</span>
<span>  <span class="va">features</span>,</span>
<span>  pseudotime.data <span class="op">=</span> <span class="st">"PCA"</span>,</span>
<span>  <span class="va">lineage</span>,</span>
<span>  magic <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  scale <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  sort <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  color_scheme <span class="op">=</span> <span class="st">"D"</span>,</span>
<span>  conda_env <span class="op">=</span> <span class="st">"seuratextend"</span></span>
<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 that has undergone pseudotime analysis with either Palantir or Slingshot, containing necessary gene expression data and pseudotime calculations.</p></dd>


<dt>features</dt>
<dd><p>A vector of gene names for which expression dynamics will be visualized in the heatmap.</p></dd>


<dt>pseudotime.data</dt>
<dd><p>The name of the slot within `seu@misc` where pseudotime data is stored or a data.frame containing pseudotime information; for Palantir, this is typically 'Pseudotime', and for Slingshot, 'PCA'.</p></dd>


<dt>lineage</dt>
<dd><p>The specific lineage or trajectory to visualize in the heatmap, which corresponds to the clusters or trajectories defined within the pseudotime analysis.</p></dd>


<dt>magic</dt>
<dd><p>Logical indicating whether to use denoised gene expression data for plotting, obtained via MAGIC. Requires prior execution of Palantir.Magic() if set to TRUE. Default: FALSE.</p></dd>


<dt>scale</dt>
<dd><p>Boolean indicating whether to scale gene expression data between 0 and 1, which can help in normalizing expression levels for better visual contrast in the heatmap. Default: TRUE.</p></dd>


<dt>sort</dt>
<dd><p>Boolean indicating whether to sort genes by expression peak along pseudotime from left to right. Default: TRUE.</p></dd>


<dt>color_scheme</dt>
<dd><p>The color scheme to use for the heatmap. Default: 'D'.</p></dd>


<dt>conda_env</dt>
<dd><p>Name of the Conda environment where necessary Python dependencies are installed for operations that require Python. Default: 'seuratextend'.</p></dd>

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

<p>A ggplot object, displaying gene expression trends along computed pseudotime trajectories by heatmap.</p>
    </div>
    <div id="details">
    <h2>Details</h2>
    <p>These visualization tools are designed to highlight gene expression changes over pseudotime, providing insights into cellular behaviors and gene regulation during differentiation processes. Each function is tailored to the specific pseudotime analysis, ensuring that visualizations are closely aligned with the underlying data and pseudotime results.</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><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>
<span><span class="co"># Load an example Seurat Object</span></span>
<span><span class="va">mye_small</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/connections.html" class="external-link">url</a></span><span class="op">(</span><span class="st">"https://zenodo.org/records/10944066/files/pbmc10k_mye_small_velocyto.rds"</span>, <span class="st">"rb"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Calculate diffusion map and pseudotime using Palantir</span></span>
<span><span class="va">mye_small</span> <span class="op">&lt;-</span> <span class="fu"><a href="Palantir-Methods.html">Palantir.RunDM</a></span><span class="op">(</span><span class="va">mye_small</span><span class="op">)</span></span>
<span><span class="va">mye_small</span> <span class="op">&lt;-</span> <span class="fu"><a href="Palantir-Methods.html">Palantir.Pseudotime</a></span><span class="op">(</span><span class="va">mye_small</span>, start_cell <span class="op">=</span> <span class="st">"sample1_GAGAGGTAGCAGTACG-1"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Customizing gene trend heatmap with Palantir</span></span>
<span><span class="va">ps</span> <span class="op">&lt;-</span> <span class="va">mye_small</span><span class="op">@</span><span class="va">misc</span><span class="op">$</span><span class="va">Palantir</span><span class="op">$</span><span class="va">Pseudotime</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">ps</span><span class="op">)</span><span class="op">[</span><span class="fl">3</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"fate1"</span>, <span class="st">"fate2"</span><span class="op">)</span></span>
<span><span class="fu">GeneTrendHeatmap.Palantir</span><span class="op">(</span></span>
<span>  <span class="va">mye_small</span>,</span>
<span>  features <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CD14"</span>, <span class="fu"><a href="https://mojaveazure.github.io/seurat-object/reference/VariableFeatures.html" class="external-link">VariableFeatures</a></span><span class="op">(</span><span class="va">mye_small</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span><span class="op">)</span>,</span>
<span>  pseudotime.data <span class="op">=</span> <span class="va">ps</span>,</span>
<span>  lineage <span class="op">=</span> <span class="st">"fate1"</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Run Slingshot</span></span>
<span><span class="va">mye_small</span> <span class="op">&lt;-</span> <span class="fu"><a href="RunSlingshot.html">RunSlingshot</a></span><span class="op">(</span><span class="va">mye_small</span>, group.by <span class="op">=</span> <span class="st">"cluster"</span>, start.clus <span class="op">=</span> <span class="st">"Mono CD14"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Using Slingshot for similar visualizations</span></span>
<span><span class="fu">GeneTrendHeatmap.Slingshot</span><span class="op">(</span></span>
<span>  <span class="va">mye_small</span>,</span>
<span>  features <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CD14"</span>, <span class="fu"><a href="https://mojaveazure.github.io/seurat-object/reference/VariableFeatures.html" class="external-link">VariableFeatures</a></span><span class="op">(</span><span class="va">mye_small</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span><span class="op">)</span>,</span>
<span>  lineage <span class="op">=</span> <span class="st">"slingPseudotime_2"</span></span>
<span><span class="op">)</span></span>
<span></span></code></pre></div>
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