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      <img src="" class="logo" alt=""><h1>Spatial feature visualization</h1>
      <small class="dont-index">Source: <a href="https://github.com/data2intelligence/SpaCET/blob/HEAD/R/visualization.R" class="external-link"><code>R/visualization.R</code></a></small>
      <div class="d-none name"><code>SpaCET.visualize.spatialFeature.Rd</code></div>
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    <div class="ref-description section level2">
    <p>Visualize multiple types of spatial features in ST data.</p>
    </div>

    <div class="section level2">
    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SpaCET.visualize.spatialFeature</span><span class="op">(</span></span>
<span>  <span class="va">SpaCET_obj</span>,</span>
<span>  spatialType <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">"QualityControl"</span>, <span class="st">"GeneExpression"</span>, <span class="st">"CellFraction"</span>, <span class="st">"LRNetworkScore"</span>,</span>
<span>    <span class="st">"Interface"</span>, <span class="st">"GeneSetScore"</span><span class="op">)</span>,</span>
<span>  spatialFeatures <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  scaleTypeForGeneExpression <span class="op">=</span> <span class="st">"LogTPM"</span>,</span>
<span>  sameScaleForFraction <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  colors <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  pointSize <span class="op">=</span> <span class="fl">1</span>,</span>
<span>  nrow <span class="op">=</span> <span class="fl">1</span>,</span>
<span>  imageBg <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  interactive <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div class="section level2">
    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
    <dl><dt>SpaCET_obj</dt>
<dd><p>An SpaCET object.</p></dd>


<dt>spatialType</dt>
<dd><p>Type of spatial features, i.e., "QualityControl", "GeneExpression", "CellFraction", "LRNetworkScore", "Interface", and "GeneSetScore". See ‘details’ for more information.</p></dd>


<dt>spatialFeatures</dt>
<dd><p>A vector of spatial features.</p></dd>


<dt>scaleTypeForGeneExpression</dt>
<dd><p>Scale type of gene expression, i.e., "RawCounts","LogRawCounts","LogTPM/10", and "LogTPM".</p></dd>


<dt>sameScaleForFraction</dt>
<dd><p>Indicate whether all cell types have the same scale for cell fraction.</p></dd>


<dt>nrow</dt>
<dd><p>Row number of the combined panel for multiple spatial features.</p></dd>


<dt>imageBg</dt>
<dd><p>logical: should the image be shown?</p></dd>

</dl></div>
    <div class="section level2">
    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
    

<p>A ggplot2 object.</p>
    </div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
    <p>`SpaCET.visualize.spatialFeature` is able to plot multiple types of spatial features, including "QC", "GeneExp", "CellFraction", and "LRNetworkScore".
"QualityControl" refers to quality control metrics. User can visualize the total counts of UMI and genes across all spots.
"GeneExpr" is set to visualize the expression level of genes.
"CellFraction" refers to the cell fraction of cell types.
"LRNetworkScore" is selected to show the Ligand-Receptor network score. See `SpaCET.CCI.LRNetworkScore` for how to calculate it.</p>
    </div>

    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SpaCET.visualize.spatialFeature</span><span class="op">(</span><span class="va">SpaCET_obj</span>, spatialType <span class="op">=</span> <span class="st">"QualityControl"</span>, spatialFeatures<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">"UMI"</span>,<span class="st">"Gene"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="fu">SpaCET.visualize.spatialFeature</span><span class="op">(</span><span class="va">SpaCET_obj</span>, spatialType <span class="op">=</span> <span class="st">"GeneExpression"</span>, spatialFeatures<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">"EPCAM"</span>,<span class="st">"MS4A1"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="fu">SpaCET.visualize.spatialFeature</span><span class="op">(</span><span class="va">SpaCET_obj</span>, spatialType <span class="op">=</span> <span class="st">"CellFraction"</span>, spatialFeatures<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">"Malignant"</span>,<span class="st">"Macrophage"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="fu">SpaCET.visualize.spatialFeature</span><span class="op">(</span><span class="va">SpaCET_obj</span>, spatialType <span class="op">=</span> <span class="st">"CellFraction"</span>, spatialFeatures<span class="op">=</span><span class="st">"All"</span>, pointSize <span class="op">=</span> <span class="fl">0.1</span>, nrow<span class="op">=</span><span class="fl">5</span><span class="op">)</span></span>
<span><span class="fu">SpaCET.visualize.spatialFeature</span><span class="op">(</span><span class="va">SpaCET_obj</span>, spatialType <span class="op">=</span> <span class="st">"LRNetworkScore"</span>, spatialFeatures<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">"Network_Score"</span>,<span class="st">"Network_Score_pv"</span><span class="op">)</span><span class="op">)</span></span>
<span></span></code></pre></div>
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