R/enhance_get_GO_data.R

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

##' @importFrom AnnotationDbi keys
##' @importFrom AnnotationDbi keytypes
##' @importFrom AnnotationDbi toTable
##' @importFrom GO.db GOTERM
##' @importFrom kit fduplicated
##' @importFrom GOSemSim load_OrgDb
##' @importFrom utils stack
enhance_get_GO_data <- function(OrgDb, ont, keytype) {
  GO_Env <- get_GO_Env()
  use_cached <- FALSE

  ont2 <- NULL
  if (exists("ont", envir = GO_Env, inherits = FALSE))
    ont2 <- get("ont", envir = GO_Env)

  if (exists("organism", envir=GO_Env, inherits=FALSE) &&
      exists("keytype", envir=GO_Env, inherits=FALSE) &&
      !is.null(ont2)) {

    org <- get("organism", envir=GO_Env)
    kt <- get("keytype", envir=GO_Env)

    if (org == get_organism(OrgDb) &&
        keytype == kt &&
        (ont == ont2 || ont2 == "ALL") &&
        exists("goAnno", envir=GO_Env, inherits=FALSE)) {
      ## https://github.com/GuangchuangYu/clusterProfiler/issues/182
      ## && exists("GO2TERM", envir=GO_Env, inherits=FALSE)){

      use_cached <- TRUE
    }
  }

  if (use_cached) {
    goAnno <- get("goAnno", envir=GO_Env)
    if (!is.null(ont2) && ont2 != ont) { ## ont2 == "ALL"
      goAnno <- goAnno[goAnno$ONTOLOGYALL == ont,]
    }
  } else {
    OrgDb <- load_OrgDb(OrgDb)
    kt <- keytypes(OrgDb)
    if (! keytype %in% kt) {
      stop("keytype is not supported...")
    }

    kk <- keys(OrgDb, keytype=keytype)

    ## --> take too much memory
    ##
    ## goAnno <- suppressMessages(
    ##     select(OrgDb, keys=kk, keytype=keytype,
    ##            columns=c("GOALL", "ONTOLOGYALL")))

    ## if (ont == "ALL") {
    ##     GO2GENE <- unique(goAnno[, c(2,1)])
    ## } else {
    ##     GO2GENE <- unique(goAnno[goAnno$ONTOLOGYALL == ont, c(2,1)])
    ## }

    goterms <- AnnotationDbi::Ontology(GO.db::GOTERM)
    if (ont != "ALL") {
      goterms <- goterms[goterms == ont]
    }
    go2gene <- suppressMessages(
      AnnotationDbi::mapIds(OrgDb, keys=names(goterms), column=keytype,
                            keytype="GOALL", multiVals='list')
    )
    goAnno <- stack(go2gene)
    colnames(goAnno) <- c(keytype, "GOALL")
    # goAnno <- unique(goAnno[!is.na(goAnno[,1]), ])
    goAnno <- goAnno[!is.na(goAnno[,1]), ]
    goAnno <- goAnno[!kit::fduplicated(goAnno),]
    goAnno$ONTOLOGYALL <- goterms[goAnno$GOALL]

    assign("goAnno", goAnno, envir=GO_Env)
    assign("keytype", keytype, envir=GO_Env)
    assign("ont", ont, envir = GO_Env)
    assign("organism", get_organism(OrgDb), envir=GO_Env)
  }

  ## if (ont == "ALL") {
  ##     GO2GENE <- unique(goAnno[, c(2,1)])
  ## } else {
  ##     GO2GENE <- unique(goAnno[goAnno$ONTOLOGYALL == ont, c(2,1)])
  ## }
  # GO2GENE <- unique(goAnno[, c(2,1)])
  GO2GENE <- goAnno[, c(2,1)]
  GO2GENE <- GO2GENE[!kit::fduplicated(GO2GENE),]

  GO_DATA <- enhance_build_Anno(GO2GENE, enhance_get_GO2TERM_table())

  # goOnt.df <- goAnno[, c("GOALL", "ONTOLOGYALL")] %>% unique
  goOnt.df <- goAnno[, c("GOALL", "ONTOLOGYALL")]
  goOnt.df <- goOnt.df[!kit::fduplicated(goOnt.df), c("GOALL", "ONTOLOGYALL")]

  if (!is.null(ont2) && ont2 == "ALL") {
    return(GO_DATA)
  }

  goOnt <- goOnt.df[,2]
  names(goOnt) <- goOnt.df[,1]
  assign("GO2ONT", goOnt, envir=GO_DATA)

  return(GO_DATA)
}

get_GO_Env <- function () {
  if (!exists(".GO_clusterProfiler_Env", envir = .GlobalEnv)) {
    pos <- 1
    envir <- as.environment(pos)
    assign(".GO_clusterProfiler_Env", new.env(), envir=envir)
  }
  get(".GO_clusterProfiler_Env", envir = .GlobalEnv)
}

enhance_get_GO2TERM_table <- function() {
  GOTERM.df <- get_GOTERM()
  x = GOTERM.df[, c("go_id", "Term")]
  x[!kit::fduplicated(x),]
}

get_organism <- DOSE:::get_organism
get_GOTERM <- clusterProfiler:::get_GOTERM