R/available_organisms.R

In ViSEAGO: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

#' @title Display available organisms from a specified database.
#' @description Display an interactive table with available organisms from a genomic ressource database (Bioconductor, EntrezGene, Ensembl, Uniprot).
#' @importFrom DT datatable
#' @family genomic_ressource
#' @family visualization
#' @param object a  \code{\link{genomic_ressource-class}} object created by \code{\link{Bioconductor2GO}}, \code{\link{EntrezGene2GO}},
#' \code{\link{Ensembl2GO}},or \code{\link{Uniprot2GO}} methods.
#' @details
#' an interactive \code{datatable}.
#' @return javascript datatable
#' @references
#'  Yihui Xie (2016). DT: A Wrapper of the JavaScript Library 'DataTables'. R package version 0.2. https://CRAN.R-project.org/package=DT
#' @include genomic_ressource.R
#' @examples
#' # display Bioconductor table
#' Bioconductor<-ViSEAGO::Bioconductor2GO()
#' ViSEAGO::available_organisms(Bioconductor)
#' \dontrun{
#'
#' # display EntrezGene table
#' EntrezGene<-ViSEAGO::EntrezGene2GO()
#' ViSEAGO::available_organisms(EntrezGene)
#'
#' # display Ensembl table
#' Ensembl<-ViSEAGO::Ensembl2GO()
#' ViSEAGO::available_organisms(Ensembl)
#'
#' # display Uniprot table
#' Uniprot<-ViSEAGO::Uniprot2GO()
#' ViSEAGO::available_organisms(Uniprot)
#' }
#' @name available_organisms
#' @rdname available_organisms-methods
#' @exportMethod available_organisms
setGeneric(
    name="available_organisms",
    def=function(object){
        standardGeneric("available_organisms")
})

#' @rdname available_organisms-methods
#' @aliases available_organisms
setMethod(
    "available_organisms",
    signature="genomic_ressource",
    definition=function(object){

        # create a datatable
        datatable(

            # table
            slot(object,"organisms"),

            # table width
            width=650,

            # filter column
            filter ='top',

            # extensions to use
            extensions =c('Scroller'),

            # DT options to use
            options=list(

                # the dom
                dom='ltipr',

                # page length
                pageLength =5,

                # y scroller
                deferRender = TRUE,
                scrollY = 200,
                scroller = TRUE
            )
        )
})