hyp_hmap: Visualize hyp/multihyp objects as a hiearchy map

In montilab/hypeR: An R Package For Geneset Enrichment Workflows

Visualize hyp/multihyp objects as a hiearchy map

Description

Visualize hyp/multihyp objects as a hiearchy map

Usage

hyp_hmap(
  hyp_obj,
  pval = 1,
  fdr = 1,
  val = c("fdr", "pval"),
  top = NULL,
  title = "",
  graph = FALSE
)

Arguments

hyp_obj	A hyp or multihyp object
pval	Filter results to be less than pval cutoff
fdr	Filter results to be less than fdr cutoff
val	Choose significance value displayed when hovering nodes e.g. c("fdr", "pval")
top	Limit number of pathways shown
title	Plot title
graph	Return an igraph object instead

Value

A visNetwork object

Examples

genesets <- hyperdb_rgsets("REACTOME", "70.0")

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_hmap(hyp_obj, top=60)

montilab/hypeR documentation built on Oct. 29, 2023, 12:01 p.m.