plot_network

Visualizes a gene regulatory or protein–protein interaction network for a given 
cell type and differential expression group. Nodes are sized and colored by degree, 
and key hub genes are optionally annotated with their barplots of log fold-changes 
across sexes.

Tools to analyze sex differences in omics data for complex diseases. It includes functions for differential expression analysis using the 'limma' method <doi:10.1093/nar/gkv007>, interaction testing between sex and disease, pathway enrichment with 'clusterProfiler' <doi:10.1089/omi.2011.0118>, and gene regulatory network (GRN) construction and analysis using 'igraph'. The package enables a reproducible workflow from raw data processing to biological interpretation.

Enrico Glaab

XYomics

Analysis of Sex Differences in Omics Data for Complex Diseases

Sophie Le Bars

Mohamed Soudy

Murodzhon Akhmedov

plot_network function

<dl><dt>g</dt>
<dd>An `igraph` object representing the gene or protein interaction network.</dd>
<dt>cell_type</dt>
<dd>Character string. The cell type label used in the plot title.</dd>
<dt>DEG_type</dt>
<dd>Character string. The differential expression category to visualize (e.g., `"sex-dimorphic"`).</dd>
<dt>result_categories</dt>
<dd>A `data.frame` or tibble containing at least the columns:
`"DEG_Type"`, `"Gene_Symbols"`, `"Male_avg_logFC"`, and `"Female_avg_logFC"`.</dd></dl>

Arguments

Plot a Condition-Specific protein-protein interaction network with DEG Annotations — plot_network

<dl>

<dt>g</dt>
<dd>An `igraph` object representing the gene or protein interaction network.</dd>


<dt>cell_type</dt>
<dd>Character string. The cell type label used in the plot title.</dd>


<dt>DEG_type</dt>
<dd>Character string. The differential expression category to visualize (e.g., `"sex-dimorphic"`).</dd>


<dt>result_categories</dt>
<dd>A `data.frame` or tibble containing at least the columns:
`"DEG_Type"`, `"Gene_Symbols"`, `"Male_avg_logFC"`, and `"Female_avg_logFC"`.</dd>

</dl>

plot_network: Plot a Condition-Specific protein-protein interaction network with DEG Annotations

Description

Usage

Value

Arguments