Visualize hyp/multihyp objects as a hiearchy map

Source: R/hyp_hmap.R

Visualize hyp/multihyp objects as a hiearchy map

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)