R/go-utilities.R

In YuLab-SMU/clusterProfiler: A universal enrichment tool for interpreting omics data

##' convert goid to descriptive term
##'
##'
##' @title go2term
##' @param goid a vector of GO IDs
##' @return data.frame
##' @export
##' @author Guangchuang Yu
go2term <- function(goid) {
    GO2TERM <- get_GO2TERM_table()
    res <- GO2TERM[GO2TERM[,1] %in% goid, ]
    rownames(res) <- NULL
    return(res)
}

##' convert goid to ontology (BP, CC, MF)
##'
##'
##' @title go2ont
##' @param goid a vector of GO IDs
##' @return data.frame
##' @export
##' @author Guangchuang Yu
go2ont <- function(goid) {
    GO2Ontology <- get_GO2Ontology_table()
    res <- GO2Ontology[GO2Ontology[,1] %in% goid,]
    rownames(res) <- NULL
    return(res)
}


get_GOTERM <- function() {
    pos <- 1
    envir <- as.environment(pos)
    if (!exists(".GOTERM_Env", envir=envir)) {
        assign(".GOTERM_Env", new.env(), envir)
    }
    GOTERM_Env <- get(".GOTERM_Env", envir = envir)
    if (exists("GOTERM.df", envir = GOTERM_Env)) {
        GOTERM.df <- get("GOTERM.df", envir=GOTERM_Env)
    } else {
        GOTERM.df <- toTable(GOTERM)
        assign("GOTERM.df", GOTERM.df, envir = GOTERM_Env)
    }
    return(GOTERM.df)
}

get_GO2TERM_table <- function() {
    GOTERM.df <- get_GOTERM()
    GOTERM.df[, c("go_id", "Term")] %>% unique
}

get_GO2Ontology_table <- function() {
    GOTERM.df <- get_GOTERM()
    GOTERM.df[, c("go_id", "Ontology")] %>% unique
}


excludeGOlevel <- function(x, ont, level) {
    lv <- unlist(lapply(level, getGOLevel, ont=ont))
    x <- excludeGOterm(x, lv)
    return(x)
}

excludeGOterm <- function(x, term) {
    if ( is(x, "enrichResult") ) {
        x@result <- x@result[! x@result[, "ID"] %in% term, ]
    } else if ( is(x, "compareClusterResult") ) {
        x@compareClusterResult <- x@compareClusterResult[! x@compareClusterResult[, "ID"] %in% term, ]
    } else {
        stop("x should be one of enrichResult of compareClusterResult...")
    }
    return(x)
}

keepGOlevel <- function(x, ont, level) {
    lv <- unlist(lapply(level, getGOLevel, ont=ont))
    x <- keepGOterm(x, lv)
    return(x)
}

keepGOterm <- function(x, term) {
    if ( is(x, "enrichResult") ) {
        x@result <- x@result[x@result[, "ID"] %in% term, ]
    } else if ( is(x, "compareClusterResult") ) {
        x@compareClusterResult <- x@compareClusterResult[x@compareClusterResult[, "ID"] %in% term, ]
    } else {
        stop("x should be one of enrichResult of compareClusterResult...")
    }
    return(x)
}

##' query GOIDs at a specific level.
##'
##'
##' @title get GOIDs at a specific level
##' @param ont Ontology
##' @param level GO level
##' @return a vector of GOIDs
##' @importFrom GO.db GOBPCHILDREN
##' @importFrom GO.db GOCCCHILDREN
##' @importFrom GO.db GOMFCHILDREN
##' @importMethodsFrom AnnotationDbi mget
##' @author Guangchuang Yu \url{https://yulab-smu.top}
##' @noRd
getGOLevel <- function(ont, level) {
    switch(ont,
           MF = {
               topNode <- "GO:0003674"
               Children <- GOMFCHILDREN
           },
           BP = {
               topNode <- "GO:0008150"
               Children <- GOBPCHILDREN
           },
           CC = {
               topNode <- "GO:0005575"
               Children <- GOCCCHILDREN
           }
           )

    max_level <- max(level)
    if (any(level == 1)) {
        all_nodes <- topNode
    } else {
        all_nodes <- c()
    }

    Node <- topNode
    for (i in seq_len(max_level-1)) {
        Node <- mget(Node, Children, ifnotfound=NA)
        Node <- unique(unlist(Node))
        Node <- as.vector(Node)
        Node <- Node[!is.na(Node)]
        if ((i+1) %in% level) {
            all_nodes <- c(all_nodes, Node)
        }
    }
    return(all_nodes)
}


add_GO_Ontology <- function(obj, GO_DATA) {
    if (is(obj, 'gseaResult')) {
        obj@setType <- "GOALL"
    } else if (is(obj, 'enrichResult')) {
        obj@ontology <- 'GOALL'
    }

    df <- obj@result
    GO2ONT <- get("GO2ONT", envir=GO_DATA)
    df <- cbind(ONTOLOGY=GO2ONT[df$ID], df)
    obj@result <- df
    return(obj)
}


get_go_ontology <- function(x) {
    if (is(x, "compareClusterResult")) {
        if (x@fun != "enrichGO" && x@fun != "groupGO" && x@fun != "gseGO") {
            stop("simplify only work for GO...")
        }
        ont <- x@.call$ont
        if (is.null(ont) || !inherits(ont, "character")) {
            ## should be "MF", default value of enrichGO
            ## it's safe to determine from the output
            ont <- x@compareClusterResult$ID[1] %>% GOTERM[[.]] %>% Ontology
        }
    } else if (is(x, "enrichResult")) {
        if (!x@ontology %in% c("BP", "MF", "CC"))
            stop("ontology should be one of 'MF', 'BP', 'CC'...")

        ont <- x@ontology
    } else {
        stop("x should be an instance of 'enrichResult' or 'compareClusterResult'...")
    }

    return(ont)
}