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<h1>NanoSIMS data processing of LANS data in R: HMR files</h1>
<small class="dont-index">Source: <a href="https://github.com/KopfLab/lans2r/blob/master/vignettes/lans2r-hmr.Rmd"><code>vignettes/lans2r-hmr.Rmd</code></a></small>
<div class="hidden name"><code>lans2r-hmr.Rmd</code></div>
</div>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(lans2r)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(knitr)</a>
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(ggplot2)</a></code></pre></div>
<p>This vignettes illustrates how to read and visualize data from HMR (=ion beam scan) files generated by the NanoSIMS software. These are primarily tuning files that are valuable for visualizing and evaluating how tuning parameters affect the peak shapes. This functionality is completely independent from LANS.</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">hmr <-<span class="st"> </span><span class="kw"><a href="../reference/load_HMR.html">load_HMR</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/system.file.html">system.file</a></span>(<span class="st">"extdata"</span>, <span class="st">"nanosims_data"</span>, <span class="st">"hmr"</span>, <span class="dt">package =</span> <span class="st">"lans2r"</span>), </a>
<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="dt">prefix =</span> <span class="st">""</span>, <span class="dt">suffix =</span> <span class="st">".hmr_txt"</span>)</a></code></pre></div>
<div id="settings-overview" class="section level4">
<h4 class="hasAnchor">
<a href="#settings-overview" class="anchor"></a>Settings overview</h4>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">hmr <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>step, <span class="op">-</span>voltage, <span class="op">-</span>cts) <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/distinct.html">distinct</a></span>() <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/knitr/man/kable.html">kable</a></span>()</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">ion</th>
<th align="left">prefix</th>
<th align="left">filename</th>
<th align="left">date</th>
<th align="left">trolley</th>
<th align="left">B</th>
<th align="left">R</th>
<th align="left">M</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1H</td>
<td align="left"></td>
<td align="left">/space/ims/data/Kopf/April_2014/PA_5e_1H.hmr</td>
<td align="left">2014-02-04 21:32:00</td>
<td align="left">#0</td>
<td align="left">998.7</td>
<td align="left">130.53</td>
<td align="left">1.025</td>
</tr>
<tr class="even">
<td align="left">2H</td>
<td align="left"></td>
<td align="left">/space/ims/data/Kopf/April_2014/PA_5e_2H.hmr</td>
<td align="left">2014-02-04 21:32:00</td>
<td align="left">#1</td>
<td align="left">998.7</td>
<td align="left">184.90</td>
<td align="left">2.056</td>
</tr>
</tbody>
</table>
</div>
<div id="scan-overview" class="section level4">
<h4 class="hasAnchor">
<a href="#scan-overview" class="anchor"></a>Scan overview</h4>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">hmr <span class="op">%>%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>() <span class="op">+</span></a>
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(voltage, cts, <span class="dt">color =</span> ion) <span class="op">+</span><span class="st"> </span></a>
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/geom_path.html">geom_line</a></span>() <span class="op">+</span></a>
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html">scale_y_log10</a></span>(<span class="st">"counts"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/facet_wrap.html">facet_wrap</a></span>(<span class="op">~</span>ion, <span class="dt">scales =</span> <span class="st">"free"</span>)</a></code></pre></div>
<p><img src="lans2r-hmr_files/figure-html/unnamed-chunk-4-1.png" width="672"></p>
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