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    <div class="page-header">
    <h1>Modified version of FeatureScatter</h1>
    <small class="dont-index">Source: <a href="https://github.com/samuel-marsh/scCustomize/blob/HEAD/R/Seurat_Plotting.R" class="external-link"><code>R/Seurat_Plotting.R</code></a></small>
    <div class="hidden name"><code>FeatureScatter_scCustom.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Create customized FeatureScatter plots with scCustomize defaults.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">FeatureScatter_scCustom</span><span class="op">(</span></span>
<span>  <span class="va">seurat_object</span>,</span>
<span>  feature1 <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  feature2 <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  colors_use <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  pt.size <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  group.by <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  split.by <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  split_seurat <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  shuffle <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  aspect_ratio <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  title_size <span class="op">=</span> <span class="fl">15</span>,</span>
<span>  plot.cor <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  num_columns <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  raster <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  raster.dpi <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="fl">512</span>, <span class="fl">512</span><span class="op">)</span>,</span>
<span>  ggplot_default_colors <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  color_seed <span class="op">=</span> <span class="fl">123</span>,</span>
<span>  <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

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


<dt>feature1</dt>
<dd><p>First feature to plot.</p></dd>


<dt>feature2</dt>
<dd><p>Second feature to plot.</p></dd>


<dt>colors_use</dt>
<dd><p>color for the points on plot.</p></dd>


<dt>pt.size</dt>
<dd><p>Adjust point size for plotting.</p></dd>


<dt>group.by</dt>
<dd><p>Name of one or more metadata columns to group (color) cells by (for example, orig.ident).
Default is active ident.</p></dd>


<dt>split.by</dt>
<dd><p>Feature to split plots by (i.e. "orig.ident").</p></dd>


<dt>split_seurat</dt>
<dd><p>logical.  Whether or not to display split plots like Seurat (shared y axis) or as
individual plots in layout.  Default is FALSE.</p></dd>


<dt>shuffle</dt>
<dd><p>logical, whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. Default is TRUE.</p></dd>


<dt>aspect_ratio</dt>
<dd><p>Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
Default is NULL.</p></dd>


<dt>title_size</dt>
<dd><p>size for plot title labels. Does NOT apply if <code>split_seurat = TRUE</code>.</p></dd>


<dt>plot.cor</dt>
<dd><p>Display correlation in plot subtitle (or title if <code>split_seurat = TRUE</code>).</p></dd>


<dt>num_columns</dt>
<dd><p>number of columns in final layout plot.</p></dd>


<dt>raster</dt>
<dd><p>Convert points to raster format.  Default is NULL which will rasterize by default if
greater than 200,000 cells.</p></dd>


<dt>raster.dpi</dt>
<dd><p>Pixel resolution for rasterized plots, passed to geom_scattermore().
Default is c(512, 512).</p></dd>


<dt>ggplot_default_colors</dt>
<dd><p>logical.  If <code>colors_use = NULL</code>, Whether or not to return plot using
default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.</p></dd>


<dt>color_seed</dt>
<dd><p>random seed for the "varibow" palette shuffle if <code>colors_use = NULL</code> and number of
groups plotted is greater than 36.  Default = 123.</p></dd>


<dt>...</dt>
<dd><p>Extra parameters passed to <code><a href="https://satijalab.org/seurat/reference/FeatureScatter.html" class="external-link">FeatureScatter</a></code>.</p></dd>

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

<p>A ggplot object</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><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="r-in"><span></span></span>
<span class="r-in"><span><span class="va">pbmc_small</span><span class="op">$</span><span class="va">sample_id</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><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">"sample1"</span>, <span class="st">"sample2"</span><span class="op">)</span>, size <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">ncol</a></span><span class="op">(</span><span class="va">pbmc_small</span><span class="op">)</span>, replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">FeatureScatter_scCustom</span><span class="op">(</span>seurat_object <span class="op">=</span> <span class="va">pbmc_small</span>, feature1 <span class="op">=</span> <span class="st">"nCount_RNA"</span>,</span></span>
<span class="r-in"><span>feature2 <span class="op">=</span> <span class="st">"nFeature_RNA"</span>, split.by <span class="op">=</span> <span class="st">"sample_id"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE: <span style="color: #00BB00;">FeatureScatter_scCustom</span> returns split plots as layout of all plots each</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> with their own axes as opposed to Seurat which returns with shared x or y axis.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> To return to Seurat behvaior set `split_seurat = TRUE`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> -----This message will be shown once per session.-----</span>
<span class="r-plt img"><img src="FeatureScatter_scCustom-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
    </div>
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