Generate enrichment map igraph (for GSEA) — enrichment_map

Helper function to generate an enrichment map based on GSEA results. Similar enriched gene sets are clustered together via their Jaccard similarity (alternatively overlap coefficient) and the function returns an igraph object for subsequent visualisations.

Usage

enrichment_map_gsea(
  res,
  threshold,
  pathways,
  overlap_coefficient = FALSE,
  min_sim = 0.2,
  resolution = 1,
  layout_func = igraph::layout_with_fr,
  ...
)

Arguments

res: data.table with the enrichment results. Needs to have the columns c("pathway_name", "nes", "fdr"), i.e. the output of bixverse::calc_fgsea() or bixverse::calc_blitzgsea(). A geneset_name column is accepted with a deprecation warning.
threshold: Numeric. The FDR threshold you wish to filter for.
pathways: Named list. The original pathway list used for the calculation of the overenrichment analysis.
overlap_coefficient: Boolean. Shall the overlap coefficient be used instead of the Jaccard similarity.
min_sim: Numeric. Minimum similarity between two gene sets to be connected.
resolution: Numeric. The resolution parameter for the Louvain clustering.
layout_func: Layout function. Please see igraph::add_layout_() for options. This one will be used to layout the graph.
...: Further parameters to forward to wrap_and_truncate().

Value

igraph object representing the enrichment map.