hyp_dots: Visualize hyp/multihyp objects as a dots plot

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

Visualize hyp/multihyp objects as a dots plot

Description

Visualize hyp/multihyp objects as a dots plot

Usage

hyp_dots(
  hyp_obj,
  top = 20,
  abrv = 50,
  size_by = c("genesets", "significance", "none"),
  pval = 1,
  fdr = 1,
  val = c("fdr", "pval"),
  title = "",
  merge = FALSE
)

Arguments

hyp_obj	A hyp or multihyp object
top	Limit number of genesets shown
abrv	Abbreviation length of geneset labels
size_by	Size dots by e.g. c("genesets", "significance", "none")
pval	Filter results to be less than pval cutoff
fdr	Filter results to be less than fdr cutoff
val	Choose significance value for plot e.g. c("fdr", "pval")
title	Plot title
merge	Use true to merge a multihyp object into one plot

Value

A ggplot object

Examples

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_dots(hyp_obj, val="fdr")

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