test/Annotation_comparison.R

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

#' @title Compares  orignal annotationd vs. auto_annotations
#' @description Gives set relatinships
#' @param set_org manula annotations
#' @param set_annot auto-annotations
#' @return List.
#' @examples
#' comp.sets(set_org, set_annot)
#'

comp.sets<-function(set_org, set_annot){
  iden_org_found=list()
  if (length(intersect(set_org, set_annot))==0) {
    iden_org_found$iden="none"
    iden_org_found$org="na"
    iden_org_found$found="na"
    if (any(set_annot %in% get_ancestors(hao.obo, set_org))==T){iden_org_found$iden="original is finer" }
  } else if (setequal(set_org, set_annot)==T) {
    iden_org_found$iden="identical"
    iden_org_found$org="na"
    iden_org_found$found="na"
  } else if ((setequal(set_org, set_annot)==F)){
    iden_org_found$org=setdiff(set_org, set_annot)
    iden_org_found$found=setdiff(set_annot, set_org)
    iden_org_found$iden="partial"
    if (all(set_org %in% set_annot)==T) {iden_org_found$iden="original is subset"}
    if (all(set_annot %in% set_org)==T) {iden_org_found$iden="auto_annot is subset"}
  }
  return(iden_org_found)
}



#' @title Compares  orignal annotationd vs. auto_annotations and returns a vector of relatinships summarized by comp.sets()
#' @description Compares  orignal annotationd vs. auto_annotations and returns a vector of relatinships summarized by comp.sets().
#' @param ontology ontology with ontology$annot_characters
#' @param annot.auto annot.auto=grep_all_chars; from grep search
#' @return Vector with relatinships; each name is a character ID.
#' @examples
#' com_lists=compare_annot(ontology, grep_all_chars)

compare_annot<-function(ontology, annot.auto){
  out.list=c()
  for (i in seq_along(annot.auto)){
    char_id=ontology$id_characters[i]
    #out.list$ids[i]=i
    if (length(ontology$annot_characters[[char_id]])>0){
      comp.list=comp.sets(ontology$annot_characters[[char_id]], annot.auto[[char_id]])
      out.list=c(out.list, comp.list$iden)
      #out.list$identical[i]=comp.list$iden
      #out.list$original_missing[[i]]=comp.list$org
      #out.list$found_missing[[i]]=comp.list$found
    }
    else out.list=c(out.list, "character abscent")
  }
  #names(out.list)<-names(ontology$id_characters)
  return(out.list)
}
#length(which(com_lists=="none"))
#cbind(com_lists)

#' @title Compares  orignal annotationd vs. auto_annotations and returns a table of comparisons
#' @description Compares  orignal annotationd vs. auto_annotations and returns a table of comparisons. depends on compare_annot()
#' @param ontology ontology with ontology$annot_characters
#' @param grep_all_chars auto annotated chars from grep search
#' @return Table.
#' @examples
#' tb_compar=get_comp_table(hao.obo, grep_all_chars)

get_comp_table<-function(ontology, grep_all_chars){
  com_lists=compare_annot(ontology, grep_all_chars)
  dt_out=c()

  for (i in seq_along(ontology$id_characters)){
    c1=char_id=ontology$id_characters[i]
    c2=ontology$name_characters[i]
    c3=ontology$annot_characters[[char_id]]
    c4=com_lists[i]
    c5=grep_all_chars[[char_id]]

    c3=paste(paste(c3, get_onto_name(c3, ontology), sep="-(", collapse="); "), ")", sep="")
    c5=paste(paste(c5, get_onto_name(c5, ontology), sep="-(", collapse="); "), ")", sep="")

    dt_out=rbind(dt_out, c(c1,c2,c3,c4,c5))
  }
  colnames(dt_out)<-c("id", "statemet", "original_annot", "compar_results", "suggested_annot")
  return(dt_out)
}

# tb_compar=get_comp_table(hao.obo, grep_all_chars)
# write.csv(tb_compar, file="auto_annatotated4.csv", row.names = F)