runOntoFast: Run ontoFAST interactively

In ontoFAST: Interactive Annotation of Characters with Biological Ontologies

Description

This function runs ontoFAST in interactive mode. Interactive mode allows character annotation and navigation through ontology network.

Usage

runOntoFast(
  is_a = c("is_a"),
  part_of = c("BFO:0000050"),
  nchar = "all",
  show.chars = TRUE,
  shiny_in = "shiny_in",
  file2save = "OntoFAST_shiny_in.RData",
  ...
)

Arguments

is_a	term for is_a relationships
part_of	term for part_of relationships
nchar	number of characters to show
show.chars	shows character statements
shiny_in	a name of ontology (shiny_in) object in "ontofast" enviroment
file2save	a name of the file to which shiny_in object is saved in interactive mode
...	other arguments

Value

runs ontoFAST interactively using Shiny.

Examples

data(Sharkey_2011)
data(HAO)
hao_obo<-onto_process(HAO, Sharkey_2011[,1], do.annot = FALSE)
ontofast <- new.env(parent = emptyenv())
ontofast$shiny_in <- make_shiny_in(hao_obo)
runOntoFast(is_a = c("is_a"), part_of = c("BFO:0000050"), shiny_in="shiny_in" )

ontoFAST documentation built on April 29, 2021, 9:06 a.m.