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 usingp_cutoff
andp_adj
.The top
n_terms
terms for each module are selected based on the Combined Score. If ties occur, thebreak_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).