R/non121_strategy_opts.R

In neurogenomics/orthogene: Interspecies gene mapping

non121_strategy_opts <- function(non121_strategy = NULL,
                                 include_agg = FALSE) {
    dbs_opts <- setNames(
        rep("dbs", 3),
        c("drop_both_species", "dbs", 1)
    )
    dis_opts <- setNames(
        rep("dis", 3),
        c("drop_input_species", "dis", 2)
    )
    dos_opts <- setNames(
        rep("dos", 3),
        c("drop_output_species", "dos", 3)
    )
    kbs_opts <- setNames(
        rep("kbs", 7),
        c(
            "keep_both_species", "kbs", 4, "keep",
            as.character(NA),
            as.character(FALSE),
            as.character(tolower(FALSE))
        )
    )
    kp_opts <- stats::setNames(rep("kp", 3), c("keep_popular", "kp", 5))
    #### Concat ####
    all_opts <- c(dbs_opts, dis_opts, dos_opts, kbs_opts, kp_opts)
    #### Aggregation options ####
    agg_opts <- check_agg_opts()
    if (include_agg) {
        all_opts <- c(all_opts, agg_opts)
    }
    #### Return all options ####
    if (is.null(non121_strategy)) {
        return(all_opts)
    } else {
        #### Query dictionary ####
        non121_strategy <- gsub(
            " ", "_",
            tolower(as.character(non121_strategy))[1]
        )
        if (non121_strategy %in% names(all_opts)) {
            return(all_opts[non121_strategy])
        } else {
            stop_msg <- paste0(
                "non121_strategy must be one of:\n",
                "  - DIS OPTS: ", paste(names(dis_opts),
                    collapse = " / "
                ), "\n",
                "  - DOS OPTS: ", paste(names(dos_opts),
                    collapse = " / "
                ), "\n",
                "  - DBS OPTS: ", paste(names(dbs_opts),
                    collapse = " / "
                ), "\n",
                "  - KBS OPTS: ", paste(names(kbs_opts),
                    collapse = " / "
                ), "\n",
                "  - KP OPTS: ", paste(names(kp_opts),
                    collapse = " / "
                ), "\n",
                if (include_agg) {
                    c(
                        "  - AGGREGATION OPTS:\n",
                        paste("    -", names(agg_opts),
                            collapse = "\n"
                        ), "\n"
                    )
                } else {
                    NULL
                }
            )
            stop(stop_msg)
        }
    }
}