test/main.R

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

install.packages()

#save ontology
#save(ontology, file="Ontology_HAO-save_before_expereminet.RData")
require("ontologyIndex")

setwd("~/my-papers-2017/phyloBayesHMM/ontoFast/ontoFast/data")
setwd("~/my-papers-2017/phyloBayesHMM/ontoFast/ontoFast/")
# creating OntologyIndex object
hao_obo=get_OBO(system.file("data_onto", "HAO.obo", package = "ontoFAST"),
                extract_tags="everything", propagate_relationships = c("BFO:0000050", "is_a"))

# creating character ids for all 392 characters
id_characters<-paste("CHAR:",c(1:392), sep="")
hao_obo$id_characters<-id_characters

# reading characters and states
#char_et_states<-read.csv("Sharkey_chars.csv", header=T,  stringsAsFactors = F, na.strings = "")
char_et_states<-Sharkey_2011

char_et_states<-read.csv(system.file("data_onto", "Sharkey_2011.csv", package = "ontoFAST"), header=T,  stringsAsFactors = F, na.strings = "")

# creating character name vector
name_characters<-char_et_states[,1]
names(name_characters)<-id_characters
hao_obo$name_characters<-name_characters

#including manual annotations !!! work on it to do better exmaple from the beginning of file reading
#hao_obo$annot_characters<-ontology$annot_characters

# pase synonyms for automatic annotation
hao_obo$parsed_synonyms<-syn_extract(hao_obo)

# automatic annotation
hao_obo$auto_annot_characters<-annot_all_chars(hao_obo, use.synonyms=TRUE, min_set=TRUE)

hao_obo<-onto_process(HAO, Sharkey_2011[,1], do.annot = F)

#shiny_in<<-c()
#make a global object
shiny_in<<-make_shiny_in(hao_obo)
#run OntoFast
runOntoFast(nchar=5, show.chars=T)
ontoFAST::runOntoFast()

HAO$synonym
#selected terms
shiny_in$terms_selected
shiny_in$terms_selected_id
names(shiny_in$terms_map[shiny_in$terms_map %in%sa])

sa<<-c()
shiny_in$auto_annot_characters[["CHAR:381"]][a]

system.file("data_onto", "HAO.obo", package = "ontoFAST")

#roxygen2::roxygenize()

save(char_et_states, file="Sharkey_chars.RData")
HAO<-hao_obo1
devtools::use_data(HAO)

devtools::build()
devtools::use_vignette("my-vignette")

devtools::use_data(exlude_terms, exlude_terms)

# vizualize

ontology$annot_characters <-ontology$auto_annot_characters
chrs_term<-chars_per_term(ontology)

terms<-get_ancestors_chars(ontology, ontology$id_characters)

get_part_descen(ontology, terms , is_a=c("is_a"), part_of=c("BFO:0000050"))


sequences <- read.csv(
  system.file("examples/visit-sequences.csv",package="sunburstR")
  ,header=F
  ,stringsAsFactors = FALSE
)

sunburst(sequences)

tb_viz<-system.file("examples/visit-sequences.csv",package="sunburstR")




test<-data.frame(id = c("a-b-3", "a-b-2", "c-d-3", "c-d-2"),count=c(1,1,1,1))
sunburst(test)


ontology_partof=get_OBO(system.file("data_onto", "HAO.obo", package = "ontoFAST"),
                extract_tags="everything", propagate_relationships = c("BFO:0000050"))

ontology=get_OBO(system.file("data_onto", "HAO.obo", package = "ontoFAST"),
                        extract_tags="everything", propagate_relationships = c("BFO:0000050", "is_a"))



chars_per_term(ontology)
ontology$annot_characters<-ontology$auto_annot_characters

ontology$ancestors[1:5]

ontology<-onto_process(ontology, Sharkey_2011[,1])



exlude_terms<-c("anatomical entity",
            "anatomical structure",
            "material anatomical entity",
            "anatomical group",
            "multi-cellular organism",
            "anatomical cluster",
            "anatomical system",
            "organism subdivision",
            "tagma",
            "acellular anatomical structure",
            "integument",
            "area",
            "cuticle",
            "body",
            "segment",
            "body segment",
            "immaterial anatomical entity",
            "anatomical line",
            "median anatomical line",
            "portion of tissue"
)

######### Read Istvan's annotations

setwd("/home/tarasov/my-papers-2017/HAO_new")
ist.annot<-read.csv("Istvan-annotations.csv", header=F,  stringsAsFactors = F, na.strings = "")
Sharkey_2011_annot<-edges2list(ist.annot)
length(ist.annot)
devtools::use_data(exclude_terms)

HAO$annot_characters<-

  load(file="shiny_in.Rdata")
exclude_terms <-exlude_terms

devtools::use_build_ignore()