Visualize hyp/multihyp objects as a dots plot

Source: R/hyp_dots.R

Visualize hyp/multihyp objects as a dots plot

hyp_dots(
  hyp_obj,
  top = 20,
  abrv = 50,
  sizes = TRUE,
  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
sizes

Size dots by geneset sizes
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")