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for two or more defined phylostratum (divergence stratum) classes the statistical significance of
the differences of mean relative expression of these two (or more) corresponding phylostratum (divergence stratum) classes.
As test-statistic, the function performs a nonparametric kruskal.test
 based on relative expression values stored within each defined phylostratum class."><meta property="og:description" content="This function takes a PhyloExpressionSet or DivergenceExpressionSet object as input and computes
for two or more defined phylostratum (divergence stratum) classes the statistical significance of
the differences of mean relative expression of these two (or more) corresponding phylostratum (divergence stratum) classes.
As test-statistic, the function performs a nonparametric kruskal.test
 based on relative expression values stored within each defined phylostratum class."><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 Mean Relative Expression Levels as Barplot</h1>
      <small class="dont-index">Source: <a href="https://github.com/drostlab/myTAI/blob/HEAD/R/PlotBarRE.R" class="external-link"><code>R/PlotBarRE.R</code></a></small>
      <div class="d-none name"><code>PlotBarRE.Rd</code></div>
    </div>

    <div class="ref-description section level2">
    <p>This function takes a PhyloExpressionSet or DivergenceExpressionSet object as input and computes
for two or more defined phylostratum (divergence stratum) classes the statistical significance of
the differences of mean relative expression of these two (or more) corresponding phylostratum (divergence stratum) classes.
As test-statistic, the function performs a nonparametric <code><a href="https://rdrr.io/r/stats/kruskal.test.html" class="external-link">kruskal.test</a></code>
 based on relative expression values stored within each defined phylostratum class.</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">PlotBarRE</span><span class="op">(</span></span>
<span>  <span class="va">ExpressionSet</span>,</span>
<span>  Groups <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  wLength <span class="op">=</span> <span class="fl">0.1</span>,</span>
<span>  ratio <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  p.adjust.method <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 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-groups">Groups<a class="anchor" aria-label="anchor" href="#arg-groups"></a></dt>
<dd><p>a list containing the phylostrata or divergence-strata that correspond to the same phylostratum class or divergence class.
For ex. evolutionary old phylostrata: PS1-3 (Class 1) and evolutionary young phylostrata: PS4-12 (Class 2).
In this case, the <code>Groups</code> list could be assigned as, <code>Groups</code> = list(c(1:3), c(4:12)).
It is also possible to define more than 2 groups of evolutionary ages.
For ex. <code>Groups</code> = list(c(1:3),c(4:8),c(9:12)) would perform a <code><a href="https://rdrr.io/r/stats/kruskal.test.html" class="external-link">kruskal.test</a></code> to determine the statistical significance
of the evolutionary classes PS1-3, PS4-6, and PS9-12 based on their corresponding mean relative expression levels.</p></dd>


<dt id="arg-wlength">wLength<a class="anchor" aria-label="anchor" href="#arg-wlength"></a></dt>
<dd><p>a numeric value defining the whiskers length above the bars. In case there are numerous different phylostratum classes
a smaller <code>wLength</code> parameter should be used for better visualizations.</p></dd>


<dt id="arg-ratio">ratio<a class="anchor" aria-label="anchor" href="#arg-ratio"></a></dt>
<dd><p>a boolean value specifying whether the bars in the barplot represent the
mean relative expression level of phylostrata belonging to the same phylostratum class.
In case <code>ratio</code> = TRUE, the ratio of the mean relative expression level of
the two phylostrata classes is plotted as lines within the barplot. This parameter can only be used for 2 class comparisons.</p></dd>


<dt id="arg-p-adjust-method">p.adjust.method<a class="anchor" aria-label="anchor" href="#arg-p-adjust-method"></a></dt>
<dd><p>correction method to adjust p-values for multiple comparisons (see <code><a href="https://rdrr.io/r/stats/p.adjust.html" class="external-link">p.adjust</a></code> for possible methods).
E.g., <code>p.adjust.method = "BH"</code> (Benjamini &amp; Hochberg (1995)) or <code>p.adjust.method = "bonferroni"</code> (Bonferroni correction).</p></dd>


<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>default graphics parameters.</p></dd>

</dl></div>
    <div class="section level2">
    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
    <p>A barplot comparing Phylostratum-Classes by its mean relative expression levels.
Significant stages are marked by '*' referring to statistically significant differences:</p>
<p>(1) '*'   = P-Value &lt;= 0.05</p>
<p>(2) '**'  = P-Value &lt;= 0.005</p>
<p>(3) '***' = P-Value &lt;= 0.0005</p>
    </div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
    <p>In case a large number of developmental stages is included in the input <code>ExpressionSet</code>,
 p-values returned by <code>PlotBarRE</code> should be adjusted for multiple comparisons which can be done
 by specifying the <code>p.adjust.method</code> argument.</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. "A transcriptomic hourglass in plant embryogenesis". Nature (490): 98-101.</p>
<p>Domazet-Loso T. and Tautz D. 2010. "A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns". Nature (468): 815-818.</p>
<p>Myles Hollander and Douglas A. Wolfe (1973), Nonparametric Statistical Methods. New York: John Wiley &amp; Sons. Pages 115-120.</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="RE.html">RE</a></code>, <code><a href="REMatrix.html">REMatrix</a></code>,<code><a href="PlotRE.html">PlotRE</a></code>, <code><a href="https://rdrr.io/r/stats/kruskal.test.html" class="external-link">kruskal.test</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="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"># example PhyloExpressionSet</span></span></span>
<span class="r-in"><span><span class="fu">PlotBarRE</span><span class="op">(</span>ExpressionSet <span class="op">=</span> <span class="va">PhyloExpressionSetExample</span>,</span></span>
<span class="r-in"><span>          Groups        <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><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">1</span><span class="op">:</span><span class="fl">3</span><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">4</span><span class="op">:</span><span class="fl">12</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="PlotBarRE-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 class="co"># example DivergenceExpressionSet</span></span></span>
<span class="r-in"><span><span class="fu">PlotBarRE</span><span class="op">(</span>ExpressionSet <span class="op">=</span> <span class="va">DivergenceExpressionSetExample</span>,</span></span>
<span class="r-in"><span>          Groups        <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><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">1</span><span class="op">:</span><span class="fl">5</span><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">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="PlotBarRE-2.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 class="co"># Perform PlotBarRE() with p-value adjustment method Benjamini &amp; Hochberg (1995)</span></span></span>
<span class="r-in"><span><span class="fu">PlotBarRE</span><span class="op">(</span>ExpressionSet   <span class="op">=</span> <span class="va">PhyloExpressionSetExample</span>,</span></span>
<span class="r-in"><span>          Groups          <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><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">1</span><span class="op">:</span><span class="fl">3</span><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">4</span><span class="op">:</span><span class="fl">12</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>          p.adjust.method <span class="op">=</span> <span class="st">"BH"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="PlotBarRE-3.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 class="co"># Example: plot ratio</span></span></span>
<span class="r-in"><span><span class="co"># the ratio curve visualizes the ratio between bar 1 / bar 2</span></span></span>
<span class="r-in"><span><span class="co"># the z - axis shows the corresponding ratio value of bar 1 / bar 2</span></span></span>
<span class="r-in"><span><span class="fu">PlotBarRE</span><span class="op">(</span>ExpressionSet <span class="op">=</span> <span class="va">PhyloExpressionSetExample</span>,</span></span>
<span class="r-in"><span>          Groups        <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><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">1</span><span class="op">:</span><span class="fl">3</span><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">4</span><span class="op">:</span><span class="fl">12</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>          ratio         <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="PlotBarRE-4.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
</code></pre></div>
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