hyp_hmap {hypeR}R Documentation

Visualize hyp/multihyp objects as a hiearchy map

Description

Visualize hyp/multihyp objects as a hiearchy map

Usage

hyp_hmap(hyp_obj, title = "", pval_cutoff = 1, fdr_cutoff = 1,
  val = c("fdr", "pval"), top = NULL, multihyp_titles = TRUE,
  show_plots = TRUE, return_plots = FALSE)

Arguments

hyp_obj

A hyp or multihyp object

title

Plot title

pval_cutoff

Filter results to be less than pval cutoff

fdr_cutoff

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

multihyp_titles

Use false to disable plot titles for multihyp objects

show_plots

Use true to show plots

return_plots

Use true to return plots

Value

A visNetwork object or list of visNetwork objects

Examples

rgsets <- hyperdb_fetch(type="rgsets", "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")

# Perform hyper enrichment
hyp_obj <- hypeR(signature, rgsets, bg=2522, fdr_cutoff=0.05)

# Visualize
hyp_hmap(hyp_obj, top=60)


[Package hypeR version 1.2.0 Index]