R/clixo-function.R

In herdiantrisufriyana/clixo: An implementation of the Clique-Extracted Ontology (CliXO) algorithm

#' Create Clique-Extracted Ontology (CliXO)
#'
#' This function create clique-extracted ontology from a similarity matrix.
#'
#' @param similarity Feature similarity, a square matrix of numerics containing
#' feature-feature similarity measures.
#' @param alpha A numeric of a noise parameter. Please see
#' https://pubmed.ncbi.nlm.nih.gov/24932003/.
#' @param beta A numeric of a parameter which deals with missing edges. Please
#' see https://pubmed.ncbi.nlm.nih.gov/24932003/.
#' @param feature_name A character to annotate feature (source)-ontology
#' (target) relation in the resulting ontology.
#' @param onto_prefix A character that precedes the resulting ontology names.
#' @param os A character of operating system. This may be 'windows',
#' 'linux', or 'mac'
#'
#' @return clique-extracted ontology, a data frame with rows for ontologies and
#' four columns for source, target, similarity, and relation. Feature (source)-
#' ontology (target) relation is annotated as 'feature' as defined by default
#' for \code{feature_name}, while ontology-ontology relation is annotated as
#' 'is_a'. To differentiate between feature and ontology names, an
#' \code{onto_prefix} with ':' precedes an ontology name. All columns except
#' similarity are characters. Similarity (a numeric) is a minimum threshold by
#' which either features or ontologies (source) belong to an ontology (target).
#'
#' @keywords clixo
#'
#' @export
#'
#' @examples
#'
#' ## Create input example
#' input=input_example()
#'
#' ## Run CliXO algorithm
#' ontology=clixo(input$similarity)

clixo=function(similarity
               ,alpha=0.01
               ,beta=0.5
               ,feature_name='feature'
               ,onto_prefix='CliXO'
               ,os='windows'){

  if(os=='windows'){
    clixo_path='clixo_0.3/clixo_0.3_windows'
  }else{
    clixo_path='clixo_0.3'
  }

  # Clone forked clixo C++ program from GitHub
  system(paste(c(
    'git clone https://github.com/herdiantrisufriyana/clixo_0.3/'
  ),collapse=' '))
  on.exit(system('rm -r clixo_0.3'))

  # Format and write similarity to tsv for input
  similarity %>%
    as.data.frame() %>%
    rownames_to_column(var='source') %>%
    gather(target,similarity,-source) %>%
    .[lower.tri(similarity) %>% as.logical(),] %>%
    arrange(desc(similarity)) %>%
    write_tsv(paste0('clixo_0.3/input.tsv',collapse=''),col_names=F)

  # Run clixo algorithm
  if(os=='windows'){
    filecon=file('clixo_0.3/ontology.cx')
    on.exit({system('rm -r clixo_0.3'); close(filecon)})
    suppressWarnings(system(paste(c(
      paste0(clixo_path,'/clixo')
      ,'clixo_0.3/input.tsv'
      ,alpha
      ,beta
      ,feature_name
    ),collapse=' '),intern=T)) %>%
      paste(collapse='\n') %>%
      writeLines(filecon)
  }else{
    system(paste(c(
      'bash -c'
      ,paste0('"',clixo_path,'/clixo')
      ,'clixo_0.3/input.tsv'
      ,alpha
      ,beta
      ,feature_name
      ,'> clixo_0.3/ontology.cx"'
    ),collapse=' '))
  }

  # Read output file into R
  cx=
    suppressMessages(suppressWarnings(read_tsv(
      'clixo_0.3/ontology.cx',
      col_names=c('target','source','relation','similarity'),
      col_types=list(
        col_character(),
        col_character(),
        col_character(),
        col_double()
      ),
      skip=sum(
        1,
        suppressMessages(
            suppressWarnings(read_tsv('clixo_0.3/ontology.cx'))
          ) %>%
          setNames('column') %>%
          filter(str_detect(column,'#')) %>%
          nrow()
      )
    ))) %>%
    mutate(
      relation=ifelse(relation=='default','is_a',feature_name),
      source=ifelse(relation=='is_a',paste0('CliXO:',source),source),
      target=paste0(onto_prefix,':',target)
    ) %>%
    select(source,target,similarity,relation)

  # Format target name
  cx$target=
    paste0(
      onto_prefix
      ,':'
      ,str_pad(
        as.numeric(
          gsub(paste0(onto_prefix,':'),'',cx$target)
        ),
        str_count(
          max(as.numeric(
            gsub(paste0(onto_prefix,':'),'',cx$target)
          ))
        ),
        'left',
        '0'
      )
    )

  # Format source name
  cx$source[cx$relation=='is_a']=
    paste0(
      onto_prefix
      ,':'
      ,str_pad(
        as.numeric(
          gsub(paste0(onto_prefix,':'),'',cx$source[cx$relation=='is_a'])
        ),
        str_count(
          max(as.numeric(
            gsub(paste0(onto_prefix,':'),'',cx$source[cx$relation=='is_a'])
          ))
        ),
        'left',
        '0'
      )
    )

  # Remove clixo C++ program
  # system('bash -c "rm -r clixo_0.3"')

  # Return
  cx
}