paths_sunburst: Return ontology paths for characters

In sergeitarasov/ontoFAST: Interactive Annotation of Characters with Biological Ontologies

Return ontology paths for characters

Description

Returns ontology paths for all characters. These paths can be used to create a sunburst plot of ontological dependencies.

Usage

paths_sunburst(
  ontology,
  annotations = "auto",
  exclude.terms = NULL,
  include.terms = NULL,
  use.chars = TRUE,
  sep = "-"
)

Arguments

ontology	ontology_index object with character annatotions included.
annotations	which annotations to use: "auto" means automatic annotations, "manual" means manual ones. Alternatively, any othe list element containing annotations can be specified.
exclude.terms	list of terms to exclude
include.terms	list of terms to include
use.chars	indicate whether character ids should be included in output
sep	separator used to delimit ontology terms

Value

Table.

Examples

ontology_partof=get_OBO(system.file("data_onto", "HAO.obo", package = "ontoFAST"),
extract_tags="everything", propagate_relationships = c("BFO:0000050"))
ontology_partof<-onto_process(ontology_partof, Sharkey_2011[,1], do.annot = F)
ontology_partof$annot_characters<-Sharkey_2011_annot
tb<-paths_sunburst(ontology_partof,
annotations = ontology_partof$annot_characters, exclude.terms=exclude_terms)
# library(sunburst)
sunburst(tb)

sergeitarasov/ontoFAST documentation built on Aug. 5, 2022, 4:20 a.m.