CalibrationCurve

Creates a calibration curve for consensus clustering.

internal

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, 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

CalibrationCurve function

<dl><dt>stability</dt>
<dd>output of <code>VariableSelection</code>,
<code>GraphicalModel</code> or <code>BiSelection</code>.</dd>
<dt>bty</dt>
<dd>character string indicating if the box around the plot should be
drawn. Possible values include: <code>"o"</code> (default, the box is drawn), or
<code>"n"</code> (no box).</dd>
<dt>xlab</dt>
<dd>label of the x-axis.</dd>
<dt>ylab</dt>
<dd>label of the y-axis.</dd>
<dt>cex.axis</dt>
<dd>font size for axes.</dd>
<dt>cex.lab</dt>
<dd>font size for labels.</dd>
<dt>cex.legend</dt>
<dd>font size for text legend entries.</dd>
<dt>pch</dt>
<dd>type of point, as in <code><a href="/link/points?package=sharp&version=1.4.6" data-mini-rdoc="sharp::points">points</a></code>.</dd>
<dt>lines</dt>
<dd>logical indicating if the points should be linked by lines. Only
used if <code>stability</code> is the output of <code>BiSelection</code> or
<code>Clustering</code>.</dd>
<dt>col</dt>
<dd>vector of colours.</dd>
<dt>legend</dt>
<dd>logical indicating if the legend should be included.</dd>
<dt>ncol</dt>
<dd>integer indicating the number of columns in the legend.</dd></dl>

Arguments

Calibration curve (internal) — CalibrationCurve

<dl>

<dt>stability</dt>
<dd>output of <code>VariableSelection</code>,
<code>GraphicalModel</code> or <code>BiSelection</code>.</dd>


<dt>bty</dt>
<dd>character string indicating if the box around the plot should be
drawn. Possible values include: <code>"o"</code> (default, the box is drawn), or
<code>"n"</code> (no box).</dd>


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


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


<dt>cex.axis</dt>
<dd>font size for axes.</dd>


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


<dt>cex.legend</dt>
<dd>font size for text legend entries.</dd>


<dt>pch</dt>
<dd>type of point, as in <code><a href='https://rdrr.io/r/graphics/points.html'>points</a></code>.</dd>


<dt>lines</dt>
<dd>logical indicating if the points should be linked by lines. Only
used if <code>stability</code> is the output of <code>BiSelection</code> or
<code>Clustering</code>.</dd>


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


<dt>legend</dt>
<dd>logical indicating if the legend should be included.</dd>


<dt>ncol</dt>
<dd>integer indicating the number of columns in the legend.</dd>

</dl>

CalibrationCurve: Calibration curve (internal)

Description

Usage

Value

Arguments