hyp_emap {hypeR}R Documentation

Visualize hyp/multihyp objects as an enrichment map

Description

Visualize hyp/multihyp objects as an enrichment map

Usage

hyp_emap(hyp_obj, title = "",
  similarity_metric = c("jaccard_similarity", "overlap_similarity"),
  similarity_cutoff = 0.2, 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

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

multihyp_titles

Use false to disable plot titles for multihyp objects

show_plots

An option to show plots

return_plots

An option to return plots

Value

A visNetwork object or list of visNetwork objects

Examples

gsets <- hyperdb_fetch(type="gsets", "KEGG_2019_Human")

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, gsets, bg=2522, fdr_cutoff=0.05)

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


[Package hypeR version 1.2.0 Index]