GObubble: GO enrichment bubble plot

In biomarble/PlantNGSTools: NGS bioinformatics tools for plants

GO enrichment bubble plot

Description

GO enrichment bubble plot

Usage

GObubble(
  dataset,
  MainTitle = "",
  onlySig = T,
  useFDR = F,
  cut = 0.05,
  top = 10,
  TrimTerm = T,
  TermWidth = 60,
  ColorScheme = "rw",
  ColorReverse = F
)

Arguments

dataset	a dataframe of GOEnrich output, with these columns: GO.ID,Term,Annotated,Significant,AllDEG,Pvalue,Class,gene
MainTitle	Plot Title
onlySig	whether plot only significant Terms
useFDR	whether use FDR to define significant
cut	p value significant threshold, if useFDR is set, FDR pvalue is used
top	top n terms used to plot in each BP/MF/CC
TrimTerm	whether to trim long term name to specific length
TermWidth	Term longest width, if TrimTerm is set, long Terms will be trimmed, otherwise wrapped into specific length
ColorScheme	Color scheme used to plot pvalue, 'ryb', 'rwb', 'ryg', 'rwg', 'rw'(default), 'bw', 'gw'
ColorReverse	whether reverse the color order

biomarble/PlantNGSTools documentation built on Feb. 8, 2024, 2:46 a.m.