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<meta property="og:description" content="This function helps to format the cluster plots from degPatterns().
It allows to control the layers and it returns a ggplot object that
can accept more ggplot functions to allow customization." />
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<h1>Plot clusters from degPattern function output</h1>
<div class="hidden name"><code>degPlotCluster.Rd</code></div>
</div>
<div class="ref-description">
<p>This function helps to format the cluster plots from <code><a href='degPatterns.html'>degPatterns()</a></code>.
It allows to control the layers and it returns a ggplot object that
can accept more ggplot functions to allow customization.</p>
</div>
<pre class="usage"><span class='fu'>degPlotCluster</span>(<span class='no'>table</span>, <span class='no'>time</span>, <span class='kw'>color</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>min_genes</span> <span class='kw'>=</span> <span class='fl'>10</span>,
<span class='kw'>process</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>points</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>boxes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>smooth</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>lines</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cluster_column</span> <span class='kw'>=</span> <span class='st'>"cluster"</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>table</th>
<td><p><code>normalized</code> element from <code><a href='degPatterns.html'>degPatterns()</a></code> output.
It can be a data.frame with the following columns in there:
<code>genes, sample, expression, cluster, xaxis_column, color_column</code>.</p></td>
</tr>
<tr>
<th>time</th>
<td><p>column name to use in the x-axis.</p></td>
</tr>
<tr>
<th>color</th>
<td><p>column name to use to color and divide the samples.</p></td>
</tr>
<tr>
<th>process</th>
<td><p>whether to process the table if it is not
ready for plotting.</p></td>
</tr>
<tr>
<th>points</th>
<td><p>Add points to the plot.</p></td>
</tr>
<tr>
<th>boxes</th>
<td><p>Add boxplot to the plot.</p></td>
</tr>
<tr>
<th>smooth</th>
<td><p>Add regression line to the plot.</p></td>
</tr>
<tr>
<th>lines</th>
<td><p>Add gene lines to the plot.</p></td>
</tr>
<tr>
<th>facet</th>
<td><p>Split figures based on cluster ID.</p></td>
</tr>
<tr>
<th>cluster_column</th>
<td><p>column name if cluster is in a column
with a different name. Usefull, to plot cluster with different
cutoffs used when grouping genes from the clustering step.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p><a href='https://ggplot2.tidyverse.org/reference/ggplot2-package.html'>ggplot2</a> object.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>humanGender</span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>SummarizedExperiment</span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>ggplot2</span>)
<span class='no'>ma</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>assays</a></span>(<span class='no'>humanGender</span>)<span class='kw'>[[</span><span class='fl'>1</span>]][<span class='fl'>1</span>:<span class='fl'>100</span>,]
<span class='no'>des</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>colData</a></span>(<span class='no'>humanGender</span>)
<span class='no'>des</span><span class='kw'>[[</span><span class='st'>"other"</span>]] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/sample.html'>sample</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"a"</span>, <span class='st'>"b"</span>), <span class='fl'>85</span>, <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>res</span> <span class='kw'><-</span> <span class='fu'><a href='degPatterns.html'>degPatterns</a></span>(<span class='no'>ma</span>, <span class='no'>des</span>, <span class='kw'>time</span><span class='kw'>=</span><span class='st'>"group"</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='st'>"other"</span>, <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> <span class='message'>Working with 100 genes.</span></div><div class='output co'>#> <span class='message'>Working with 71 genes after filtering: minc > 15</span></div><div class='output co'>#> <span class='message'>Joining, by = "merge"</span></div><div class='output co'>#> <span class='message'>Joining, by = "merge"</span></div><div class='input'><span class='fu'>degPlotCluster</span>(<span class='no'>res</span>$<span class='no'>normalized</span>, <span class='st'>"group"</span>, <span class='st'>"other"</span>)</div><div class='img'><img src='degPlotCluster-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>degPlotCluster</span>(<span class='no'>res</span>$<span class='no'>normalized</span>, <span class='st'>"group"</span>, <span class='st'>"other"</span>, <span class='kw'>lines</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='img'><img src='degPlotCluster-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>tidyr</span>)</div><div class='output co'>#> <span class='message'></span>
#> <span class='message'>Attaching package: ‘tidyr’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:S4Vectors’:</span>
#> <span class='message'></span>
#> <span class='message'> expand</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>tibble</span>)
<span class='no'>table</span> <span class='kw'><-</span> <span class='fu'><a href='https://tibble.tidyverse.org/reference/rownames.html'>rownames_to_column</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span>(<span class='no'>ma</span>), <span class='st'>"genes"</span>) <span class='kw'>%>%</span>
<span class='fu'><a href='https://tidyr.tidyverse.org/reference/gather.html'>gather</a></span>(<span class='st'>"sample"</span>, <span class='st'>"expression"</span>, -<span class='no'>genes</span>) <span class='kw'>%>%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/join.html'>right_join</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/distinct.html'>distinct</a></span>(<span class='no'>res</span>$<span class='no'>df</span>[,<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"genes"</span>, <span class='st'>"cluster"</span>)]),
<span class='kw'>by</span> <span class='kw'>=</span> <span class='st'>"genes"</span>) <span class='kw'>%>%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/join.html'>left_join</a></span>(<span class='fu'><a href='https://tibble.tidyverse.org/reference/rownames.html'>rownames_to_column</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span>(<span class='no'>des</span>), <span class='st'>"sample"</span>),
<span class='kw'>by</span> <span class='kw'>=</span> <span class='st'>"sample"</span>) <span class='kw'>%>%</span>
<span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span>()
<span class='fu'>degPlotCluster</span>(<span class='no'>table</span>, <span class='st'>"group"</span>, <span class='st'>"other"</span>, <span class='kw'>process</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='degPlotCluster-3.png' alt='' width='700' height='433' /></div></pre>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#examples">Examples</a></li>
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