hyp_dots {hypeR}R Documentation

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, sizes = TRUE,
  pval_cutoff = 1, fdr_cutoff = 1, val = c("fdr", "pval"),
  title = "", multihyp_titles = TRUE, show_plots = TRUE,
  return_plots = 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_cutoff

Filter results to be less than pval cutoff

fdr_cutoff

Filter results to be less than fdr cutoff

val

Choose significance value e.g. c("fdr", "pval")

title

Plot title

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 ggplot object

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_dots(hyp_obj, top=3, val="fdr")


[Package hypeR version 1.2.0 Index]