hyp_emap: Visualize hyp/multihyp objects as an enrichment map

Description Usage Arguments Value Examples

Description

Visualize hyp/multihyp objects as an enrichment map

Usage

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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

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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.