Ridge Plot of Bootstrap Enrichment Results for Terms of Interest

This function creates a ridge plot visualizing the distribution of intersection sizes (TP) for specified terms of interest from bootstrap enrichment results.

Usage

ridge_bootstraps(enrich_res, terms_of_interest, condition = NULL)

Arguments

enrich_res: A data frame containing the enrichment results per bootstrap, including columns for Term, n (TP), and fraction.
terms_of_interest: A character vector specifying the terms of interest to be plotted.
condition: Optional. A character string specifying a particular condition to filter the enrichment results. If NULL (the default), results from all conditions will be included.

Value

A ggplot object displaying the ridge plot of intersection sizes for the specified terms of interest.

Details

The function filters the enrichment results to include only the specified terms of interest and creates a ridge plot showing the distribution of intersection sizes (TP). The terms are labeled with their names and the fraction of bootstraps in which they appear, and the plot includes quantile lines to indicate distribution quartiles.

Examples

if (FALSE) { # \dontrun{
data("example_ORA_obj")
data("example_ORA_custom_universe")
input_scm = example_ORA_obj$scmatrix
conds = example_ORA_obj$conditions
cond_x = "U"
cond_y = "F"
ORA_obj <- initEnrichment(
  scmatrix = input_scm,
  conditions = conds,
  enrichment_type = "ORA",
  annot_db = "HMDB",
  consider_isomers = TRUE,
  consider_isobars = TRUE,
  polarization_mode = "positive",
  background_type = "sub_class",
  molecule_type = "Metabo",
  condition.x = cond_x,
  condition.y = cond_y
)
ORA_res <- Run_enrichment(
  object = ORA_obj,
  custom_universe = example_ORA_custom_universe,
  report_ambiguity_scores = TRUE,
  DE_LFC_cutoff = 0,
  min.pct.diff = 0
)
multi_cond_res = collapse_ORA_boot_multi_cond(ORA_boot_res_list = ORA_res)
p4 = ridge_bootstraps(enrich_res = multi_cond_res$unfiltered_enrich_res,
                     terms_of_interest = c(multi_cond_res$clean_enrich_res$Term),
                     condition = "upregulated")
} # }