hyp_emap: Visualize hyp/multihyp objects as an enrichment map

In hypeR: An R Package For Geneset Enrichment Workflows

Description

Visualize hyp/multihyp objects as an enrichment map

Usage

hyp_emap(
  hyp_obj,
  similarity_metric = c("jaccard_similarity", "overlap_similarity"),
  similarity_cutoff = 0.2,
  pval = 1,
  fdr = 1,
  val = c("fdr", "pval"),
  top = NULL,
  title = ""
)

Arguments

hyp_obj	A hyp or multihyp object
similarity_metric	Metric to calculate geneset similarity
similarity_cutoff	Geneset similarity cutoff
pval	Filter results to be less than pval cutoff
fdr	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
title	Plot title

Value

A visNetwork object

Examples

genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")

signature <- c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502",
               "PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC",
               "IDH2","IDH1","OGDHL","PC","SDHA","SUCLG1","SUCLA2","SUCLG2")

hyp_obj <- hypeR(signature, genesets, background=2522)

hyp_emap(hyp_obj, top=30, val="fdr")

hypeR documentation built on Nov. 8, 2020, 8:19 p.m.