EnrichrBarPlot: EnrichrBarPlot

In smorabit/hdWGCNA: hdWGCNA

EnrichrBarPlot

Description

Generates bar plots from Enrichr data to visualize enriched terms for hdWGCNA modules in a Seurat object. The function outputs a PDF file for each module, with separate bar plots for each database.

Usage

EnrichrBarPlot(
  seurat_obj,
  outdir = "enrichr_plots",
  n_terms = 25,
  p_cutoff = 0.05,
  p_adj = TRUE,
  plot_size = c(6, 15),
  logscale = FALSE,
  plot_bar_color = NULL,
  plot_text_color = NULL,
  wgcna_name = NULL
)

Arguments

seurat_obj	A Seurat object
outdir	A string specifying the directory where the output PDF files will be saved. Default is "enrichr_plots".
n_terms	An integer indicating the number of top enriched terms to include in each bar plot. Default is 25.
p_cutoff	A numeric value specifying the significance threshold for including terms (p-value or adjusted p-value). Only terms with p-values below this threshold are plotted. Default is 0.05.
p_adj	Logical indicating whether to use the adjusted p-value (default: TRUE) or raw p-value for filtering terms.
plot_size	A numeric vector of length 2 specifying the width and height of the output PDF files in inches. Default is c(6, 15).
logscale	Logical specifying whether to log-transform the enrichment scores before plotting. Default is FALSE.
plot_bar_color	A string specifying the color of the bars in the bar plots. If NULL (default), bars are colored according to the module's assigned color.
plot_text_color	A string specifying the color of the text labels on the bar plots. If NULL (default), the color is automatically determined based on the bar color.
wgcna_name	The name of the hdWGCNA experiment in the seurat_obj@misc slot

Details

This function processes the Enrichr output stored in a Seurat object, filters enriched terms by significance, and generates bar plots for each WGCNA module. Separate plots are created for each database included in the Enrichr results. The top enriched terms for each module and database are ordered by their combined enrichment score. If there are ties in the enrichment scores, the function uses all tied terms.

The bar plot text and bar colors can be customized, and plots can be saved with log-transformed enrichment scores if specified. Text wrapping is applied to long term names for better readability.

Value

Generates PDF files in the specified output directory, with one file per WGCNA module. Each file contains bar plots for all databases associated with that module.

smorabit/hdWGCNA documentation built on Jan. 14, 2025, 11:29 a.m.