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and divergence-stratum values of a given PhyloExpressionSet and DivergenceExpressionSet.
This function can be used to test whether a given PS distribution and DS distribution are
linear correlated so that the independence of PS and DS can be assumed for
subsequent analyses (Quint et al., 2012)."><meta property="og:description" content="This function plots the correlation coefficient between phylostratum values
and divergence-stratum values of a given PhyloExpressionSet and DivergenceExpressionSet.
This function can be used to test whether a given PS distribution and DS distribution are
linear correlated so that the independence of PS and DS can be assumed for
subsequent analyses (Quint et al., 2012)."><meta property="og:image" content="https://drostlab.github.io/myTAI/logo.png"></head><body>
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      <img src="../logo.png" class="logo" alt=""><h1>Plot the Correlation Between Phylostrata and Divergence Strata</h1>
      <small class="dont-index">Source: <a href="https://github.com/drostlab/myTAI/blob/HEAD/R/PlotCorrelation.R" class="external-link"><code>R/PlotCorrelation.R</code></a></small>
      <div class="d-none name"><code>PlotCorrelation.Rd</code></div>
    </div>

    <div class="ref-description section level2">
    <p>This function plots the correlation coefficient between phylostratum values
and divergence-stratum values of a given PhyloExpressionSet and DivergenceExpressionSet.</p>
<p>This function can be used to test whether a given PS distribution and DS distribution are
linear correlated so that the independence of PS and DS can be assumed for
subsequent analyses (Quint et al., 2012).</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">PlotCorrelation</span><span class="op">(</span></span>
<span>  <span class="va">PhyloExpressionSet</span>,</span>
<span>  <span class="va">DivergenceExpressionSet</span>,</span>
<span>  method <span class="op">=</span> <span class="st">"pearson"</span>,</span>
<span>  linearModel <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  xlab <span class="op">=</span> <span class="st">"Phylostratum"</span>,</span>
<span>  ylab <span class="op">=</span> <span class="st">"Divergencestratum"</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-phyloexpressionset">PhyloExpressionSet<a class="anchor" aria-label="anchor" href="#arg-phyloexpressionset"></a></dt>
<dd><p>a standard PhyloExpressionSet object.</p></dd>


<dt id="arg-divergenceexpressionset">DivergenceExpressionSet<a class="anchor" aria-label="anchor" href="#arg-divergenceexpressionset"></a></dt>
<dd><p>a standard DivergenceExpressionSet object.</p></dd>


<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
<dd><p>a character string specifying the correlation method to cbe used, e.g. "pearson", "kendall", "spearman".</p></dd>


<dt id="arg-linearmodel">linearModel<a class="anchor" aria-label="anchor" href="#arg-linearmodel"></a></dt>
<dd><p>a boolean value specifying whether a linear model should be
fitted to the data and furthermore, should be visualized in the corresponding plot.</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>

</dl></div>
    <div class="section level2">
    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
    <p>a jitter-correlation-plot of PS and DS correlation.</p>
    </div>
    <div class="section level2">
    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
    <p>Quint M et al. (2012). <em>A transcriptomic hourglass in plant embryogenesis</em>. Nature (490): 98-101.
Drost HG et al. (2015) <em>Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis</em>. Mol Biol Evol. 32 (5): 1221-1231 doi:10.1093/molbev/msv012.</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="https://rdrr.io/r/stats/cor.html" class="external-link">cor</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 class="co"># read standard phylotranscriptomics data</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"># plot the PS and DS correlation</span></span></span>
<span class="r-in"><span><span class="fu">PlotCorrelation</span><span class="op">(</span><span class="va">PhyloExpressionSetExample</span>, </span></span>
<span class="r-in"><span>                <span class="va">DivergenceExpressionSetExample</span>, </span></span>
<span class="r-in"><span>                method      <span class="op">=</span> <span class="st">"pearson"</span>, </span></span>
<span class="r-in"><span>                linearModel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> `geom_smooth()` using formula = 'y ~ s(x, bs = "cs")'</span>
<span class="r-plt img"><img src="PlotCorrelation-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
    </div>
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