.enrichment_map {hypeR}R Documentation

Plot enrichment map

Description

Plot enrichment map

Usage

.enrichment_map(hyp_df, gsets, title,
  similarity_metric = c("jaccard_similarity", "overlap_similarity"),
  similarity_cutoff = 0.2, pval_cutoff = 1, fdr_cutoff = 1,
  val = c("fdr", "pval"), top = NULL)

Arguments

hyp_df

A dataframe from a hyp object

gsets

A list of genesets

title

Plot title

similarity_metric

Metric to calculate geneset similarity

similarity_cutoff

Geneset similarity cutoff

pval_cutoff

Filter results to be less than pval cutoff

fdr_cutoff

Filter results to be less than fdr cutoff

val

Choose significance value shown above nodes e.g. c("fdr", "pval")

top

Limit number of pathways shown

Value

A visNetwork object


[Package hypeR version 1.2.0 Index]