Skip to contents

EnrichrDotPlot

Source: R/plotting.R
EnrichrDotPlot.Rd

Generate a dot plot visualizing enrichment results from Enrichr for hdWGCNA modules.

Usage

EnrichrDotPlot(
  seurat_obj,
  database,
  mods = "all",
  n_terms = 3,
  p_cutoff = 0.05,
  p_adj = TRUE,
  break_ties = TRUE,
  term_size = 10,
  wgcna_name = NULL
)

Arguments

seurat_obj

A Seurat object

database

A character string specifying the name of the Enrichr database to use (e.g., "GO_Biological_Process_2021").

mods

A character vector specifying the names of modules to include in the plot. If mods = "all" (default), all modules except the "grey" module are included.

n_terms

An integer specifying the number of top enriched terms to plot for each module (default = 3).

p_cutoff

A numeric value specifying the p-value threshold for filtering enriched terms (default = 0.05).

p_adj

A logical value indicating whether to use adjusted p-values (TRUE, default) or raw p-values (FALSE) for filtering.

break_ties

A logical value indicating whether to randomly select among tied terms to enforce n_terms (default = TRUE).

term_size

A numeric value specifying the font size of the enriched terms displayed on the y-axis (default = 10).

wgcna_name

The name of the hdWGCNA experiment in the seurat_obj@misc slot

Value

A ggplot2 object representing the dot plot of enriched terms for the specified modules and database.

Details

This function creates dot plots from Enrichr results associated with hdWGCNA modules. Each module is represented by its most enriched terms from the specified Enrichr database. The size of the dots indicates the enrichment score, and the color indicates the statistical significance (-log10 transformed p-value).

  • The function first retrieves WGCNA module and Enrichr data from the specified Seurat object.

  • Modules are filtered based on the mods parameter, and enriched terms are filtered by significance using p_cutoff and p_adj.

  • The top n_terms terms for each module are selected based on the Combined Score. If ties occur, the break_ties parameter determines how they are resolved.

  • A dot plot is generated where each dot represents an enriched term, its size corresponds to the Combined Score (log-transformed), and its color indicates the significance (-log10 transformed p-value).