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      <img src="../logo.png" class="logo" alt=""><h1>Plot Cumulative Transcriptome Index</h1>
      <small class="dont-index">Source: <a href="https://github.com/drostlab/myTAI/blob/HEAD/R/PlotContribution.R" class="external-link"><code>R/PlotContribution.R</code></a></small>
      <div class="d-none name"><code>PlotContribution.Rd</code></div>
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    <div class="ref-description section level2">
    <p>This function computes the cumulative contribution of each Phylostratum or Divergence Stratum to the global <code><a href="TAI.html">TAI</a></code> or <code><a href="TDI.html">TDI</a></code> profile.</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">PlotContribution</span><span class="op">(</span></span>
<span>  <span class="va">ExpressionSet</span>,</span>
<span>  legendName <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  xlab <span class="op">=</span> <span class="st">"Ontogeny"</span>,</span>
<span>  ylab <span class="op">=</span> <span class="st">"Transcriptome Index"</span>,</span>
<span>  main <span class="op">=</span> <span class="st">""</span>,</span>
<span>  y.ticks <span class="op">=</span> <span class="fl">10</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 id="arg-expressionset">ExpressionSet<a class="anchor" aria-label="anchor" href="#arg-expressionset"></a></dt>
<dd><p>a standard PhyloExpressionSet or DivergenceExpressionSet object.</p></dd>


<dt id="arg-legendname">legendName<a class="anchor" aria-label="anchor" href="#arg-legendname"></a></dt>
<dd><p>a character string specifying whether "PS" or "DS" are used to compute relative expression profiles.</p></dd>


<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a></dt>
<dd><p>label of x-axis.</p></dd>


<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a></dt>
<dd><p>label of y-axis.</p></dd>


<dt id="arg-main">main<a class="anchor" aria-label="anchor" href="#arg-main"></a></dt>
<dd><p>main title.</p></dd>


<dt id="arg-y-ticks">y.ticks<a class="anchor" aria-label="anchor" href="#arg-y-ticks"></a></dt>
<dd><p>a numeric value specifying the number of ticks to be drawn on the y-axis.</p></dd>

</dl></div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
    <p>Introduced by Domazet-Loso and Tautz (2010), this function allows users to visualize the cumulative contribution of each Phylostratum or Divergence Stratum to the global Transcriptome Age Index or Transcriptome Divergence Index profile to quantify how each Phylostratum or Divergence Stratum influences the profile of the global TAI or TDI pattern.</p>
    </div>
    <div class="section level2">
    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
    <p>Domazet-Loso T. and Tautz D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (468): 815-818.</p>
    </div>
    <div class="section level2">
    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
    <div class="dont-index"><p><code><a href="pTAI.html">pTAI</a></code>, <code><a href="pTDI.html">pTDI</a></code>, <code><a href="TAI.html">TAI</a></code>, <code><a href="TDI.html">TDI</a></code>, <code><a href="PlotSignature.html">PlotSignature</a></code></p></div>
    </div>
    <div class="section level2">
    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
    <p>Hajk-Georg Drost</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 class="r-in"><span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">PhyloExpressionSetExample</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">DivergenceExpressionSetExample</span><span class="op">)</span></span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> <span class="co"># visualize phylostratum contribution to global TAI</span></span></span>
<span class="r-in"><span> <span class="fu">PlotContribution</span><span class="op">(</span><span class="va">PhyloExpressionSetExample</span>, legendName <span class="op">=</span> <span class="st">"PS"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="PlotContribution-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> <span class="co"># visualize divergence stratum contribution to global TDI</span></span></span>
<span class="r-in"><span> <span class="fu">PlotContribution</span><span class="op">(</span><span class="va">DivergenceExpressionSetExample</span>, legendName <span class="op">=</span> <span class="st">"DS"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="PlotContribution-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span> </span></span>
</code></pre></div>
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