plotNode

This function plots all connections (incoming and outgoing) of a specific node in one network or in all network in the discovered model.

Unsupervised Bayesian network-based clustering of multi-omics data. Both binary and continuous data types
are allowed as inputs. The package serves a dual purpose: it clusters (patient) samples and learns the multi-omics networks that characterize discovered
clusters. Prior network knowledge (e.g., public interaction databases) can be included via blacklisting and
penalization matrices. For clustering, the EM algorithm is employed. For structure search at the M-step,
the Bayesian approach is used. The output includes membership assignments of samples, cluster-specific MAP networks, and posterior probabilities
of all edges in the discovered networks. In addition to likelihood, AIC and BIC scores are returned. They can be used for choosing the number
of clusters.
References:
P. Suter et al. (2021) <doi:10.1101/2021.12.16.473083>,
J. Kuipers and P. Suter and G. Moffa (2022) <doi:10.1080/10618600.2021.2020127>,
J. Kuipers et al. (2018) <doi:10.1038/s41467-018-06867-x>.

Polina Suter

bnClustOmics

Bayesian Network-Based Clustering of Multi-Omics Data

Jack Kuipers

plotNode function

<dl><dt>localint</dt>
<dd>an annotated list of interactions obtained by the function annotateEdges</dd>
<dt>node</dt>
<dd>center node name</dd>
<dt>p</dt>
<dd>defines a threshold for the posterior probability; edges whose posterior is higher than the threshold will be plotted</dd>
<dt>rmult</dt>
<dd>defines the raduis of the circle</dd>
<dt>dbcheck</dt>
<dd>logical, defines if interactions absent in the database are denoted with a dashed line</dd>
<dt>cex</dt>
<dd>regulates font size</dd></dl>

Arguments

Author

Plotting all connections of one node — plotNode

<dl>

<dt>localint</dt>
<dd>an annotated list of interactions obtained by the function annotateEdges</dd>


<dt>node</dt>
<dd>center node name</dd>


<dt>p</dt>
<dd>defines a threshold for the posterior probability; edges whose posterior is higher than the threshold will be plotted</dd>


<dt>rmult</dt>
<dd>defines the raduis of the circle</dd>


<dt>dbcheck</dt>
<dd>logical, defines if interactions absent in the database are denoted with a dashed line</dd>


<dt>cex</dt>
<dd>regulates font size</dd>

</dl>

plotNode: Plotting all connections of one node

Description

Usage

Value

Arguments

Author

Examples