dev_ontology.R

In jrboyd/ssvRecipes: Recipes using seqsetvis

BiocManager::install("GO.db", version = "3.14")
library(GO.db)
sessionInfo()
get_GO_info = function(go_ids, include_children = FALSE, include_parents = FALSE, includes_genes = FALSE, org.db = NULL, gene_name2go = NULL){
    go_df = as.data.frame(select(GO.db, go_ids, columns(GO.db)))
    if(include_children){
        all_children = lapply(go_ids, get_all_children.no_parents)
        go_df$CHILDREN = sapply(all_children, paste, collapse = ",")
        
    }
    if(include_parents){
        all_parents = lapply(go_ids, get_parents)
        go_df$PARENTS = sapply(all_parents, paste, collapse = ",")
    }
    if(includes_genes){
        if(!is.null(org.db)){
            message(paste(
                sep = "\n  ",
                "org.db must be provided. Examples:", 
                "org.Hs.eg.db",
                "org.Mm.eg.db",
                "org.Dm.eg.db"
            ))
        }
        if(is.null(gene_name2go)){
            message("making gene_name2go.  Supply result of get_gene_name2go(org.db) to save time.")
            gene_name2go = get_gene_name2go(org.db)
        }
        all_children = lapply(go_ids, get_all_children)
        all_genes = lapply(all_children, get_GO_gene_names, gene_name2go = gene_name2go)
        go_df$GENES = sapply(all_genes, paste, collapse = ",")
    }
    go_df
}

search_GO_by_term = function(search_term){
    sel = subset(select(GO.db, keys(GO.db), columns(GO.db)), grepl(search_term, TERM))
    sel_go = sel$GOID
    sel_go
}

get_parents = function(children_go){
    parent_result = annotate::getGOParents(children_go)
    parent_go = lapply(parent_result, function(x)x$Parents)
    parent_go = lapply(parent_go, function(x)x[names(x) == "is_a"])
    found_go = unlist(parent_go)
    names(found_go) = NULL
    found_go
}

get_all_children = function(parent_go, ko_go = character(), depth = 1, as.list = FALSE){
    if(as.list){
        names(parent_go) = parent_go
        lapply(parent_go, function(go){
            get_all_children(go, as.list = FALSE)
        })
    }else{
        child_result = annotate::getGOChildren(parent_go)
        children_go = unlist(lapply(child_result, function(x)x$Children))
        found_go = union(parent_go, ko_go)
        if(is.null(children_go)){
            return(found_go)
        }
        children_go.new = setdiff(children_go, found_go)
        get_all_children(children_go.new, found_go, depth = depth + 1)
    }
}

get_all_children.no_parents = function(parent_go, as.list = FALSE){
    if(as.list){
        names(parent_go) = parent_go
        lapply(parent_go, function(go){
            get_all_children.no_parents(go, as.list = FALSE)
        })
    }else{
        all_go = get_all_children(parent_go)
        setdiff(all_go, parent_go)
    }
}

get_gene_name2go = function(org.db = org.Hs.eg.db::org.Hs.eg.db){
    entrez2go = select(org.db, keys= keys(org.db), columns = c("GO")) 
    entrez2gene_name = select(org.db, keys= keys(org.db), columns = c("SYMBOL"))
    gene_name2go = merge(entrez2go, entrez2gene_name, by = 'ENTREZID')  
    gene_name2go
}

get_GO_gene_names = function(go_ids, org.db = org.Hs.eg.db::org.Hs.eg.db, as.list = FALSE, gene_name2go = NULL){
    if(is.null(gene_name2go)){
        message("making gene_name2go.  Supply result of get_gene_name2go(org.db) to save time.")
        gene_name2go = get_gene_name2go(org.db)
    }
    
    
    go_df = as.data.frame(subset(gene_name2go, GO %in% go_ids))
    if(as.list){
        split(go_df$SYMBOL, go_df$GO)    
    }else{
        unique(go_df$SYMBOL)
    }
    
}

sel_go = search_GO_by_term("activation of MAPK")
sel_go.all = get_all_children(sel_go)

gene_name2go = get_gene_name2go(org.db = org.Hs.eg.db::org.Hs.eg.db)

get_GO_gene_names(sel_go.all, gene_name2go = gene_name2go, as.list = TRUE)

library(org.Hs.eg.db)
entrez2go = select(org.Hs.eg.db, keys= keys(org.Hs.eg.db), columns = c("GO"))
entrez2gene_name = select(org.Hs.eg.db, keys= keys(org.Hs.eg.db), columns = c("SYMBOL"))
head(entrez2go)
head(entrez2gene_name)



seqsetvis::ssvFeatureVenn(
    list(
        parents = subset(gene_name2go, GO %in% sel_go)$SYMBOL,
        children = subset(gene_name2go, GO %in% setdiff(sel_go.all, sel_go))$SYMBOL 
        
    )
)



select(GO.db, sel_go, tc)
# select(GO.db, sel_go.children, tc)
select(GO.db, sel_go.all, tc)




library(annotate)

keys(org.Hs.egGENENAME)
mappedkeys(org.Hs.egGENENAME)

keys(org.Hs.egGO)
columns(org.Hs.egGO)