cp_utils.R

install_package("clusterProfiler")


## todo move to diffex commons
guess_cp_species <- function(ensIds){
    an_id <-ensIds[1]

    if(str_detect(an_id, "ENSG")){
        return("human")
    }else if(str_detect(an_id, "ENSMUSG")){
        return("mouse")
    }else if(str_detect(an_id, "ENSDARG")){
        return("zebrafish")
    }else if(str_detect(an_id, "FBgn")){
        return("fly")
    }else{
        stop(paste("could not clusterProfiler species name from ", an_id))
    }
}

guess_anno_db <- function(ensIds){
    an_id <-ensIds[1]

    if(str_detect(an_id, "ENSG")){
        return("org.Hs.eg.db")
    }else if(str_detect(an_id, "ENSMUSG")){
        return("org.Mm.eg.db")
    }else if(str_detect(an_id, "ENSDARG")){
        return("org.Dr.eg.db")
    }else if(str_detect(an_id, "FBgn")){
        return("org.Dm.eg.db")
    }else{
        stop(paste("could not anno db mart from ", an_id))
    }
}

#source("http://bioconductor.org/biocLite.R")
#biocLite("org.Mm.eg.db")
#biocLite("org.Hs.eg.db")
#biocLite("org.Dr.eg.db")
#biocLite("org.Dm.eg.db")
#biocLite("KEGG.db")
#biocLite("ReactomePA")



#load_pack(ReactomePA)


## clusterProfiler convenience wrapper for ensembl ids
find_enr_terms = function(ensemblIds, ...){
    #browser()
    annoDb = guess_anno_db(ensemblIds)
    clusterProfiler::bitr(ensemblIds, fromType="ENSEMBL", toType="ENTREZID", OrgDb=annoDb) %>%
        with(cp_test(ENTREZID, annoDb=annoDb, cp_species=guess_cp_species(ensemblIds), ...))
}


## does not work because of dots
#find_enr_terms_cached = function(ensemblIds, ...){
#    quote({find_enr_terms(ensemblIds, ...)}) %>% cache_it(paste0("cp_id_cache", digest(ensemblIds)))
#}


cp_test = function(geneIds, annoDb, cp_species, q_cutoff=0.05){
    # DEBUG geneIds <- glMapped %>% filter(cluster %in% c("cluster_9")) %$% entrez_gene_id %>% as.integer
    # DEBUG geneIds <- glMapped %>% filter(cluster_id %in% c("nr1")) %$% entrez_gene_id %>% as.integer
    # DEBUG geneIds <- head(glMapped,30)$entrez_gene_id
    #    geneIds=.$entrez_gene_id