ModuleRegulatoryNetworkPlot: ModuleRegulatoryNetworkPlot

In smorabit/hdWGCNA: hdWGCNA

ModuleRegulatoryNetworkPlot

Description

This function visualizes the regulatory network between gene modules from a Seurat object. The plot displays transcription factor (TF) regulatory interactions between modules, with edges representing positive or negative regulatory links.

Usage

ModuleRegulatoryNetworkPlot(
  seurat_obj,
  feature = "delta",
  TFs_only = TRUE,
  layout = "umap",
  umap_background = FALSE,
  max_val = 1,
  cutoff = 0,
  focus_source = NULL,
  focus_target = NULL,
  loops = TRUE,
  label_modules = TRUE,
  high_color = "orange2",
  mid_color = "white",
  low_color = "dodgerblue",
  wgcna_name = NULL,
  ...
)

Arguments

seurat_obj	A Seurat object containing single-cell data and WGCNA results.
feature	A character string specifying the type of regulatory score to plot. Options are 'positive' (positive regulatory score), 'negative' (negative regulatory score), or 'delta' (difference between positive and negative scores). Default is 'delta'.
TFs_only	Logical; if TRUE (default), only transcription factor (TF) genes are included in the plot. If FALSE, all genes are considered in the regulatory network.
layout	A character string specifying the layout for the plot. Default is 'umap', which arranges the modules according to UMAP coordinates. Other layout options from ggraph can also be used.
umap_background	Logical; if TRUE, the UMAP of module eigengenes is plotted in the background (if layout = 'umap'). Default is FALSE.
max_val	Numeric; sets the maximum absolute value for the regulatory score. Any values exceeding this threshold are capped. Default is 1.
cutoff	Numeric; edges with absolute regulatory scores below this value are excluded from the plot. Default is 0.
focus_source	Character vector; optionally restricts the plot to only show regulatory links from specified source modules. Default is NULL (all modules included).
focus_target	Character vector; optionally restricts the plot to only show regulatory links targeting specified modules. Default is NULL (all modules included).
loops	Logical; if TRUE (default), loops (self-regulatory connections) are shown in the plot.
label_modules	Logical; if TRUE (default), module names are displayed as labels in the plot.
high_color	Character string; the color representing high regulatory scores in the color gradient. Default is 'orange2'.
mid_color	Character string; the color representing intermediate regulatory scores in the color gradient. Default is 'white'.
low_color	Character string; the color representing low regulatory scores in the color gradient. Default is 'dodgerblue'.
wgcna_name	The name of the hdWGCNA experiment in the seurat_obj@misc slot
...	Additional arguments passed to the ggraph::create_layout function.

Details

The function visualizes the regulatory network between gene modules by plotting transcription factor regulatory interactions. Positive and negative regulatory scores are displayed as edges connecting nodes (modules), with node sizes proportional to the number of genes in each module. Users can customize the network layout (e.g., UMAP or other graph layouts), filter edges based on score thresholds, and highlight specific modules by using the focus parameters. Edge colors represent the strength and direction (positive or negative) of regulatory interactions, and loops can optionally be plotted to indicate self-regulation.

Value

A ggplot2 object visualizing the regulatory network, which can be further customized or displayed using plot().

smorabit/hdWGCNA documentation built on Oct. 23, 2024, 11:19 p.m.