Enrichment map — enrichment

This functions calculates similarities between gene-sets and plot a resulting enrichment map

Usage

enrichment_map(
  gs_scores = NULL,
  gene_set_sim = NULL,
  min_sim = 0.2,
  clustering_f = cluster_fast_greedy,
  min_comp_size = 1,
  gs_size = NULL,
  verbose = TRUE
)

Arguments

gs_scores: named vector of pathway scores
gene_set_sim: gene set similarity calculated through calc_gs_sim()
min_sim: threshold for the similarity score between two gene sets
clustering_f: graph clustering function, igraph::cluster_fast_greedy() by default
min_comp_size: minimum size of a community to be considered in the enrichment map then all gene-sets are displayed
gs_size: named vector with size of the gene-sets in gs_scores
verbose: verbosity

Details

enrichment_map() function calculates similarities between each gene-set pair by using method metric. Subsequently, these similarities are filtered to maintain the ones >= min_sim. clustering_f function is then used to identify communities, which may be filtered to plot only the ones composed by at least min_comp_size gene-sets.