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    <div class="page-header">
    <h1>Iterative Barcode Rank Plots</h1>
    <small class="dont-index">Source: <a href="https://github.com/samuel-marsh/scCustomize/blob/HEAD/R/QC_Plotting_Seq_10X.R" class="external-link"><code>R/QC_Plotting_Seq_10X.R</code></a></small>
    <div class="hidden name"><code>Iterate_Barcode_Rank_Plot.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Read data, calculate <code><a href="https://rdrr.io/pkg/DropletUtils/man/barcodeRanks.html" class="external-link">DropletUtils::barcodeRanks</a></code>, create barcode rank plots, and outout single PDF output.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">Iterate_Barcode_Rank_Plot</span><span class="op">(</span></span>
<span>  <span class="va">dir_path_h5</span>,</span>
<span>  multi_directory <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  h5_filename <span class="op">=</span> <span class="st">"raw_feature_bc_matrix.h5"</span>,</span>
<span>  cellranger_multi <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  parallel <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  num_cores <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  file_path <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  file_name <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  pt.size <span class="op">=</span> <span class="fl">6</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">1024</span>, <span class="fl">1024</span><span class="op">)</span>,</span>
<span>  plateau <span class="op">=</span> <span class="cn">NULL</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>dir_path_h5</dt>
<dd><p>path to parent directory (if <code>multi_directory = TRUE</code>) or directory containing
all h5 files (if <code>multi_directory = FALSE</code>).</p></dd>


<dt>multi_directory</dt>
<dd><p>logical, whether or not all h5 files are in their own subdirectories or in a
single directory (default is TRUE; each in own subdirectory (e.g. output from Cell Ranger)).</p></dd>


<dt>h5_filename</dt>
<dd><p>Either the file name of h5 file (if <code>multi_directory = TRUE</code>) or the shared
suffix (if <code>multi_directory = FALSE</code>)</p></dd>


<dt>cellranger_multi</dt>
<dd><p>logical, whether the outputs to be read are from Cell Ranger <code>multi</code> as opposed
to Cell Ranger <code>count</code> (default is FALSE).  Only valid if <code>multi_directory = FALSE</code>.</p></dd>


<dt>parallel</dt>
<dd><p>logical, should files be read in parallel (default is FALSE).</p></dd>


<dt>num_cores</dt>
<dd><p>Number of cores to use in parallel if <code>parallel = TRUE</code>.</p></dd>


<dt>file_path</dt>
<dd><p>file path to use for saving PDF output.</p></dd>


<dt>file_name</dt>
<dd><p>Name of PDF output file.</p></dd>


<dt>pt.size</dt>
<dd><p>point size for plotting, default is 6.</p></dd>


<dt>raster_dpi</dt>
<dd><p>Pixel resolution for rasterized plots, passed to geom_scattermore().
Default is c(1024, 1024).</p></dd>


<dt>plateau</dt>
<dd><p>numerical values at which to add vertical line designating estimated
empty droplet plateau (default is NULL).  Must be vector equal in length to number of samples.</p></dd>


<dt>...</dt>
<dd><p>Additional parameters passed to <code>Read10X_h5_Multi_Directory</code> or <code>Read10X_h5_GEO</code>.</p></dd>

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

<p>pdf document</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><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="r-in"><span><span class="fu">Iterate_Barcode_Rank_Plot</span><span class="op">(</span>dir_path_h5 <span class="op">=</span> <span class="st">"H5_PATH/"</span>, multi_directory <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
<span class="r-in"><span>h5_filename <span class="op">=</span> <span class="st">"raw_feature_bc_matrix"</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span>, num_cores <span class="op">=</span> <span class="fl">12</span>, file_path <span class="op">=</span> <span class="st">"OUTPUT_PATH"</span>,</span></span>
<span class="r-in"><span>file_name <span class="op">=</span> <span class="st">"Barcode_Rank_Plots"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
    </div>
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