R/helper.R

In zgzhao/gmetab: syzMetab: R package for metabolic network analysis

#' @title general helper function
#' @description general helpers for retrieving data from KDataSet, reactions list or mgraph object
#' @name helpers_general
#' @aliases Organism Species Compounds Chemicals Reactions Genes
#' @details All functions below are generic functions. Function names are self-explanatory:
#' - pathInfo(object): pathway info
#' - Organism(object): organism name
#' - Species(object): alias of Organism
#' - Genes(object): all genes/orthologs
#' - Compounds(object): all compounds
#' - Chemicals(object): alias of Compounds
#' - Reactions(object, list.only=TRUE): reactions list or ReactionSet object (list.only=FALSE for mgraph object)
#' @examples
#' library(syzMetab)
#' d.path <- file.path(path.package("syzMetab"), "KEGG")
#' pp <- make_kdset("ko00010", d.path)
#' ##
#' ## KEGG pathway data
#' pathInfo(pp)
#' Organism(pp)
#' Compounds(pp)
#' Chemicals(pp)
#' Genes(pp)
#' Reactions(pp)
#' ##
#' ## metabolic graph
#' gg <- make_mgraph(pp)
#' Organism(gg)
#' Compounds(gg)
#' Chemicals(gg)
#' Genes(gg)
#' Reactions(gg)
#' Reactions(gg, list.only=FALSE)
#' @author ZG Zhao
NULL

#' @export
setGeneric("pathInfo", function(object) standardGeneric("pathInfo"))
#' @export
setGeneric("Genes", function(object) standardGeneric("Genes"))
#' @export
setGeneric("Compounds", function(object) standardGeneric("Compounds"))
#' @export
Chemicals <- function(...) Compounds(...)
#' @export
setGeneric("Reactions", function(object, ...) standardGeneric("Reactions"))
#' @export
setGeneric("Organism", function(object) standardGeneric("Organism"))
#' @export
Species <- function(...) Organism(...)
#' @export
setGeneric("Substrates", function(object) standardGeneric("Substrates"))
#' @export
setGeneric("Substrates<-", function(object, value) standardGeneric("Substrates<-"))
#' @export
setGeneric("Products", function(object) standardGeneric("Products"))
#' @export
setGeneric("Products<-", function(object, value) standardGeneric("Products<-"))

## pathInfo =========================================
setMethod("pathInfo", "KDataSet", function(object){
    object@pathInfo
})

## Organism/Species ==================================
setMethod("Organism", "KDataSet", function(object){
    object@pathInfo$org
})
setMethod("Organism", "ReactionSet", function(object){
    object@organism
})
setMethod("Organism", "xgraph", function(object){
    x <- attr(object, "reactions")
    x@organism
})

## Reactions ==================================
setMethod("Reactions", "KDataSet", function(object){
    object@reactions
})
setMethod("Reactions", "ReactionSet", function(object){
    object@reaction
})
setMethod("Reactions", "xgraph", function(object, list.only=TRUE){
    if(is.bgraph(object)) return(NULL)
    x <- attr(object, "reactions")
    if(list.only) return(x@reaction)
    else return(x)
})

## Compounds/Chemicals ==================================
setMethod("Compounds", "KDataSet", function(object){
    rx <- sapply(Reactions(object), FUN=function(x) x[c("substrate", "product")])
    rx <- sort(unique(unlist(rx)))
    names(rx) <- NULL
    return(rx)
})
setMethod("Compounds", "ReactionList", function(object){
    rx <- sapply(object, FUN=function(x) x[c("substrate", "product")])
    rx <- sort(unique(unlist(rx)))
    names(rx) <- NULL
    return(rx)
})
setMethod("Compounds", "ReactionSet", function(object){
    rx <- sapply(Reactions(object), FUN=function(x) x[c("substrate", "product")])
    rx <- sort(unique(unlist(rx)))
    names(rx) <- NULL
    return(rx)
})
setMethod("Compounds", "xgraph", function(object){
    if(is.bgraph(object)) return(NULL)
    rx <- sapply(Reactions(object), FUN=function(x) x[c("substrate", "product")])
    rx <- sort(unique(unlist(rx)))
    names(rx) <- NULL
    return(rx)
})

## Genes ==================================
setMethod("Genes", "KDataSet", function(object){
    rx <- sapply(object@reactions, FUN=function(x) x[["gene"]])
    rx <- sort(unique(unlist(rx)))
    names(rx) <- NULL
    return(rx)
})
setMethod("Genes", "ReactionList", function(object){
    rx <- sapply(object, FUN=function(x) x[["gene"]])
    rx <- sort(unique(unlist(rx)))
    names(rx) <- NULL
    return(rx)
})
setMethod("Genes", "ReactionSet", function(object){
    rx <- sapply(object@reaction, FUN=function(rr) rr[["gene"]])
    rx <- sort(unique(unlist(rx)))
    names(rx) <- NULL
    return(rx)
})
setMethod("Genes", "xgraph", function(object){
    if(is.bgraph(object)) return(NULL)
    rtns <- Reactions(object)
    rx <- sapply(rtns, FUN=function(rr) rr[["gene"]])
    rx <- unlist(rx)
    sort(unique(rx))
})

## Substrates and products ==================================
setMethod("Substrates", "xgraph", function(object){
    attr(object, "substrates")
})

setMethod("Products", "xgraph", function(object){
    attr(object, "products")
})

setReplaceMethod("Substrates", c("xgraph", "character"),
                 function(object, value){
    attr(object, "substrates") <- value
    object
})
setReplaceMethod("Products", c("xgraph", "character"),
                 function(object, value){
    attr(object, "products") <- value
    object
})