WeightBoxplot

Creates a boxplots of the distribution of (calibrated) median attribute
weights obtained from the COSA algorithm across the subsampling iterations.
See examples in <code>Clustering</code>.

In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>) and consensus clustering (S Monti et al (2003) <doi:10.1023/A:1023949509487>), resampling techniques are used to enhance the reliability of the results. In this package (B Bodinier et al (2025) <doi:10.18637/jss.v112.i05>), hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2023a) <doi:10.1093/jrsssc/qlad058> and B Bodinier et al (2023b) <doi:10.1093/bioinformatics/btad635>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.

Barbara Bodinier

sharp

Stability-enHanced Approaches using Resampling Procedures

WeightBoxplot function

<dl><dt>stability</dt>
<dd>output of <code>Clustering</code>.</dd>
<dt>at</dt>
<dd>coordinates along the x-axis (more details in
<code><a href="/link/boxplot?package=sharp&version=1.4.7" data-mini-rdoc="sharp::boxplot">boxplot</a></code>).</dd>
<dt>argmax_id</dt>
<dd>optional indices of hyper-parameters. If
<code>argmax_id=NULL</code>, the calibrated hyper-parameters are used.</dd>
<dt>col</dt>
<dd>optional vector of colours.</dd>
<dt>boxwex</dt>
<dd>box width (more details in <code><a href="/link/boxplot?package=sharp&version=1.4.7" data-mini-rdoc="sharp::boxplot">boxplot</a></code>).</dd>
<dt>xlab</dt>
<dd>label of the x-axis.</dd>
<dt>ylab</dt>
<dd>label of the y-axis.</dd>
<dt>cex.lab</dt>
<dd>font size for labels.</dd>
<dt>las</dt>
<dd>orientation of labels on the x-axis (see
<code><a href="/link/par?package=sharp&version=1.4.7" data-mini-rdoc="sharp::par">par</a></code>).</dd>
<dt>frame</dt>
<dd>logical indicating if the box around the plot should be drawn
(more details in <code><a href="/link/boxplot?package=sharp&version=1.4.7" data-mini-rdoc="sharp::boxplot">boxplot</a></code>).</dd>
<dt>add</dt>
<dd>logical indicating if the boxplot should be added to the current
plot.</dd>
<dt>...</dt>
<dd>additional parameters passed to <code><a href="/link/boxplot?package=sharp&version=1.4.7" data-mini-rdoc="sharp::boxplot">boxplot</a></code>).</dd></dl>

Arguments

Stable attribute weights — WeightBoxplot

<dl>

<dt>stability</dt>
<dd>output of <code>Clustering</code>.</dd>


<dt>at</dt>
<dd>coordinates along the x-axis (more details in
<code><a href='https://rdrr.io/r/graphics/boxplot.html'>boxplot</a></code>).</dd>


<dt>argmax_id</dt>
<dd>optional indices of hyper-parameters. If
<code>argmax_id=NULL</code>, the calibrated hyper-parameters are used.</dd>


<dt>col</dt>
<dd>optional vector of colours.</dd>


<dt>boxwex</dt>
<dd>box width (more details in <code><a href='https://rdrr.io/r/graphics/boxplot.html'>boxplot</a></code>).</dd>


<dt>xlab</dt>
<dd>label of the x-axis.</dd>


<dt>ylab</dt>
<dd>label of the y-axis.</dd>


<dt>cex.lab</dt>
<dd>font size for labels.</dd>


<dt>las</dt>
<dd>orientation of labels on the x-axis (see
<code><a href='https://rdrr.io/r/graphics/par.html'>par</a></code>).</dd>


<dt>frame</dt>
<dd>logical indicating if the box around the plot should be drawn
(more details in <code><a href='https://rdrr.io/r/graphics/boxplot.html'>boxplot</a></code>).</dd>


<dt>add</dt>
<dd>logical indicating if the boxplot should be added to the current
plot.</dd>


<dt>...</dt>
<dd>additional parameters passed to <code><a href='https://rdrr.io/r/graphics/boxplot.html'>boxplot</a></code>).</dd>

</dl>

WeightBoxplot: Stable attribute weights

Description

Usage

Value

Arguments

See Also