node_boxplot

This function is for internal use of <code>View_diffnetworks</code>

Performs multi-omic differential network
analysis by revealing differential interactions between molecular entities
(genes, proteins, transcription factors, or other biomolecules) across the
omic datasets provided.
For each omic dataset, a differential network is constructed where
links represent statistically significant differential interactions between
entities. These networks are then integrated into a comprehensive visualization
using distinct colors to distinguish interactions from different omic layers.
This unified display allows interactive exploration of cross-omic
patterns, such as differential interactions present at both transcript and
protein levels. For each link, users can access differential statistical
significance metrics (p values or adjusted p values, calculated via robust or
traditional linear regression with interaction term) and differential regression
plots.
The methods implemented in this package are described in Sciacca et al. (2023)
<doi:10.1093/bioinformatics/btad192>.

Elisabetta Sciacca

multiDEGGs

Multi-Omic Differentially Expressed Gene-Gene Pairs

Myles Lewis

node_boxplot function

<dl><dt>gene</dt>
<dd>gene name (must be in <code>rownames(assayData)</code>)</dd>
<dt>assayDataName</dt>
<dd>name of the assayData of interest. If an unnamed list of
data was given to <code>get_diffNetworks</code>, the assayDataName here will be the
number indicating the position of the data in the assayDataList provided
before (i.e. if the user wants to plot a differential interaction observed in
the transcriptomic data, which was second in the list, then assayDataName
must be 2, if only one data table was provided assayDataName must be 1).
Default 1.</dd>
<dt>deggs_object</dt>
<dd>an object of class <code>deggs</code> generated by
<code>get_diffNetworks</code></dd></dl>

Arguments

Boxplots of single nodes (genes,proteins, etc.) — node_boxplot

<dl>

<dt>gene</dt>
<dd>gene name (must be in <code>rownames(assayData)</code>)</dd>


<dt>assayDataName</dt>
<dd>name of the assayData of interest. If an unnamed list of
data was given to <code>get_diffNetworks</code>, the assayDataName here will be the
number indicating the position of the data in the assayDataList provided
before (i.e. if the user wants to plot a differential interaction observed in
the transcriptomic data, which was second in the list, then assayDataName
must be 2, if only one data table was provided assayDataName must be 1).
Default 1.</dd>


<dt>deggs_object</dt>
<dd>an object of class <code>deggs</code> generated by
<code>get_diffNetworks</code></dd>

</dl>

node_boxplot: Boxplots of single nodes (genes,proteins, etc.)

Description

Usage

Value

Arguments