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<meta property="og:title" content="Heatmap for class biotmle — heatmap_ic" />
<meta property="og:description" content="Heatmap of contributions of a select subset of biomarkers to the variable
importance measure changes as assessed by influence curve-based estimation,
across all subjects. The heatmap produced performs supervised clustering, as
per Pollard &amp;amp; van der Laan (2008) &amp;lt;doi:10.2202/1544-6115.1404&amp;gt;." />




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    <div class="page-header">
    <h1>Heatmap for class biotmle</h1>
    <small class="dont-index">Source: <a href='https://github.com/nhejazi/biotmle/blob/master/R/plots.R'><code>R/plots.R</code></a></small>
    <div class="hidden name"><code>heatmap_ic.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Heatmap of contributions of a select subset of biomarkers to the variable
importance measure changes as assessed by influence curve-based estimation,
across all subjects. The heatmap produced performs supervised clustering, as
per Pollard &amp; van der Laan (2008) &lt;doi:10.2202/1544-6115.1404&gt;.</p>
    </div>

    <pre class="usage"><span class='fu'>heatmap_ic</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span>, <span class='va'>design</span>, FDRcutoff <span class='op'>=</span> <span class='fl'>0.25</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"top"</span>, <span class='st'>"all"</span><span class='op'>)</span>, top <span class='op'>=</span> <span class='fl'>25</span><span class='op'>)</span></pre>

    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
    <table class="ref-arguments">
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>x</th>
      <td><p>Object of class <code>biotmle</code> as produced by an appropriate call
to <code>biomarkertmle</code>.</p></td>
    </tr>
    <tr>
      <th>...</th>
      <td><p>additional arguments passed to <code><a href='https://rdrr.io/pkg/superheat/man/superheat.html'>superheat::superheat</a></code> as
necessary</p></td>
    </tr>
    <tr>
      <th>design</th>
      <td><p>A vector giving the contrast to be displayed in the heatmap.</p></td>
    </tr>
    <tr>
      <th>FDRcutoff</th>
      <td><p>Cutoff to be used in controlling the False Discovery Rate.</p></td>
    </tr>
    <tr>
      <th>type</th>
      <td><p>A <code>character</code> describing whether to plot only a top number
(as defined by FDR-corrected p-value) of biomarkers or all biomarkers.</p></td>
    </tr>
    <tr>
      <th>top</th>
      <td><p>Number of identified biomarkers to plot in the heatmap.</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>heatmap (from <span class="pkg">superheat</span>) using hierarchical clustering to plot
 the changes in the variable importance measure for all subjects across a
 specified top number of biomarkers.</p>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='cn'>FALSE</span><span class='op'>)</span> <span class='op'>{</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://dplyr.tidyverse.org'>dplyr</a></span><span class='op'>)</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>biotmleData</span><span class='op'>)</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://bioconductor.org/packages/SummarizedExperiment'>SummarizedExperiment</a></span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>illuminaData</span><span class='op'>)</span>

<span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>colData</a></span><span class='op'>(</span><span class='va'>illuminaData</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>colData</a></span><span class='op'>(</span><span class='va'>illuminaData</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
  <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>age <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/numeric.html'>as.numeric</a></span><span class='op'>(</span><span class='va'>age</span> <span class='op'>&gt;</span> <span class='fu'><a href='https://rdrr.io/r/stats/median.html'>median</a></span><span class='op'>(</span><span class='va'>age</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
  <span class='fu'>DataFrame</span><span class='op'>(</span><span class='op'>)</span>
<span class='va'>benz_idx</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/which.html'>which</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>colData</a></span><span class='op'>(</span><span class='va'>illuminaData</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%in%</span> <span class='st'>"benzene"</span><span class='op'>)</span>

<span class='va'>biomarkerTMLEout</span> <span class='op'>&lt;-</span> <span class='fu'><a href='biomarkertmle.html'>biomarkertmle</a></span><span class='op'>(</span>
  se <span class='op'>=</span> <span class='va'>illuminaData</span>,
  varInt <span class='op'>=</span> <span class='va'>benz_idx</span>,
  bppar_type <span class='op'>=</span> <span class='fu'>BiocParallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/pkg/BiocParallel/man/SerialParam-class.html'>SerialParam</a></span><span class='op'>(</span><span class='op'>)</span>,
  g_lib <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SL.mean"</span>, <span class='st'>"SL.glm"</span><span class='op'>)</span>,
  Q_lib <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SL.mean"</span>, <span class='st'>"SL.glm"</span><span class='op'>)</span>
<span class='op'>)</span>

<span class='va'>limmaTMLEout</span> <span class='op'>&lt;-</span> <span class='fu'><a href='modtest_ic.html'>modtest_ic</a></span><span class='op'>(</span>biotmle <span class='op'>=</span> <span class='va'>biomarkerTMLEout</span><span class='op'>)</span>

<span class='fu'>heatmap_ic</span><span class='op'>(</span>x <span class='op'>=</span> <span class='va'>limmaTMLEout</span>, design <span class='op'>=</span> <span class='va'>design</span>, FDRcutoff <span class='op'>=</span> <span class='fl'>0.05</span>, top <span class='op'>=</span> <span class='fl'>10</span><span class='op'>)</span>
<span class='op'>}</span>
</div></pre>
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