fortify_matrix.MAF

By default, it calls <code><a href="/link/as.matrix()?package=ggalign&version=0.0.5" data-mini-rdoc="ggalign::as.matrix()">as.matrix()</a></code> to build a matrix.

A 'ggplot2' extension offers various tools for organizing and arranging plots.
It is designed to consistently align a specific axis across multiple 'ggplot' objects,
making it especially useful for plots requiring data order manipulation. A typical use
case includes organizing combinations like a dendrogram and a heatmap.

Yun Peng

ggalign

A 'ggplot2' Extension for Consistent Axis Alignment

fortify_matrix.MAF function

<dl><dt>data</dt>
<dd>An object to be converted to a matrix.</dd>
<dt>...</dt>
<dd>Not used currently.</dd>
<dt>genes</dt>
<dd>An atomic character defines the genes to draw.</dd>
<dt>n_top</dt>
<dd>A single number indicates how many top genes to be drawn.</dd>
<dt>remove_empty_samples</dt>
<dd>A single boolean value indicating whether to drop
samples without any genomic alterations.</dd>
<dt>collapse_vars</dt>
<dd>A single boolean value indicating whether to collapse
multiple alterations in the same sample and gene into a single value
<code>"Multi_Hit"</code>.</dd></dl>

Arguments

<ul>
<li><code>gene_anno</code>: gene summary informations</li>
<li><code>sample_anno</code>: sample summary informations</li>
<li><code>n_genes</code>: Total of genes</li>
<li><code>n_samples</code>: Total of samples</li>
<li><code>breaks</code>: factor levels of <code>Variant_Classification</code>, if <code>collapse_vars = TRUE</code>, <code>"Multi_Hit"</code> will be added in the end.</li>
</ul>

ggalign attributes

By default, it calls <code><a href='https://rdrr.io/r/base/matrix.html'>as.matrix()</a></code> to build a matrix.

Build a Matrix — fortify_matrix.MAF

<dl>

<dt>data</dt>
<dd>An object to be converted to a matrix.</dd>


<dt>...</dt>
<dd>Not used currently.</dd>


<dt>genes</dt>
<dd>An atomic character defines the genes to draw.</dd>


<dt>n_top</dt>
<dd>A single number indicates how many top genes to be drawn.</dd>


<dt>remove_empty_samples</dt>
<dd>A single boolean value indicating whether to drop
samples without any genomic alterations.</dd>


<dt>collapse_vars</dt>
<dd>A single boolean value indicating whether to collapse
multiple alterations in the same sample and gene into a single value
<code>"Multi_Hit"</code>.</dd>

</dl>

<ul>
<li><code>gene_anno</code>: gene summary informations</li>
<li><code>sample_anno</code>: sample summary informations</li>
<li><code>n_genes</code>: Total of genes</li>
<li><code>n_samples</code>: Total of samples</li>
<li><code>breaks</code>: factor levels of <code>Variant_Classification</code>, if <code>collapse_vars = TRUE</code>, <code>"Multi_Hit"</code> will be added in the end.</li>
</ul>

fortify_matrix.MAF: Build a Matrix

Description

Usage

Value

Arguments

ggalign attributes

See Also