PlotDifferentialRegulons: PlotDifferentialRegulons

View source: R/Regulons.R

PlotDifferentialRegulonsR Documentation

PlotDifferentialRegulons

Description

Function to visualize differential TF regulon activity between two groups of cells based on regulon scores. The plot shows the average log fold-change (logFC) for positive and negative regulon scores in a scatter plot, with the points colored by their associated module and optionally labeled with the most differentially active regulons.

Usage

PlotDifferentialRegulons(
  seurat_obj,
  dregs,
  n_label = 10,
  logfc_thresh = 0.1,
  lm = TRUE,
  wgcna_name = NULL
)

Arguments

seurat_obj

A Seurat object that contains the WGCNA experiment and TF regulon scores.

dregs

Dataframe output from the FindDifferentialRegulons function containing differential regulon results.

n_label

Integer specifying the number of top up- and down-regulated regulons to label on the plot. If 'all', all significant regulons will be labeled. Default = 10.

logfc_thresh

Numeric threshold for labeling and annotating regulons based on logFC values. Default = 0.1.

lm

Logical indicating whether to plot a linear regression line for the logFC values of positive vs. negative regulons. Default = TRUE.

wgcna_name

The name of the WGCNA experiment in the seurat_obj@misc slot. Default is the active WGCNA experiment.

Details

This function generates a scatter plot where each point represents a TF regulon, with the x-axis showing the average log fold-change for positive regulon scores and the y-axis showing the average log fold-change for negative regulon scores. Points are colored by their module assignment, and the size of the points reflects the module eigengene correlation (kME) value of the TF.

Differentially expressed regulons can be highlighted, and the most significantly up- and down-regulated regulons can be labeled. Additional options allow adding a linear regression line and controlling label density based on logFC thresholds.

Value

A ggplot object representing the differential regulon scatter plot.


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