R/gtoxLoadWaid.R

In GladiaTOX: R Package for Processing High Content Screening data

#####################################################################
## This program is distributed in the hope that it will be useful, ##
## but WITHOUT ANY WARRANTY; without even the implied warranty of  ##
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the    ##
## GNU General Public License for more details.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# gtoxLoadWaid: Load well annotation information
#-------------------------------------------------------------------------------

#' @title Load well annotation information
#'
#' @description
#' \code{gtoxLoadWaid} queries the gtox database and returns the well annotation
#' information for the given field and values.
#'
#' @param fld Character, the field(s) to query on
#' @param val List, vectors of values for each field to query on. Must be in
#' the same order as 'fld'.
#'
#' @examples
#' ## Store the current config settings, so they can be reloaded at the end 
#' ## of the examples
#' conf_store <- gtoxConfList()
#' gtoxConfDefault()
#' 
#' ## Prepare for analysis before QC + process data
#' gtoxLoadWaid()
#' 
#' ## Reset configuration
#' options(conf_store)
#' 
#' @return A data.table with the well annotation information for the given
#' parameters
#'
#' @import data.table
#' @export

gtoxLoadWaid <- function(fld=NULL, val=NULL) {

    if (!is.null(fld)) {
        vfield <- c(
            "apid", "aid", "date_plate", "date_treat", "date_harvest",
            "cell_passage", "cell_lot", "waid", "spid", "rowi", "coli",
            "wllt", "vhid", "conc", "gui_sample_id"
        )
        if (!all(fld %in% vfield)) stop("Invalid 'fld' value(s).")
    }

    qformat <-
        "
        SELECT
            assay_plate_well.waid,
            assay_plate_well.apid,
            aid,
            spid,
            rowi,
            coli,
            wllt,
            vhid,
            conc,
            date_plate,
            date_treat,
            date_harvest,
            cell_passage,
            cell_lot,
            gui_sample_id,
            hr_barcode,
            old_name,
            s_sampleid,
            u_boxtrack
        FROM assay_plate_well
            LEFT JOIN assay_plate
                ON assay_plate_well.apid=assay_plate.apid
            LEFT JOIN bb_waid_map
                ON assay_plate_well.waid=bb_waid_map.waid
            LEFT JOIN bb_apid_map
                ON assay_plate_well.apid=bb_apid_map.apid
    "

    if (!is.null(fld)) {

        fld <- .prepField(
            fld=fld,
            tbl=c("assay_plate", "assay_plate_well"),
            db=options()$TCPL_DB
        )

        qformat <- paste(qformat, "WHERE")
        qformat <- paste0(
            qformat,
            "  ",
            paste(fld, "IN (%s)", collapse=" AND ")
        )
        qformat <- paste0(qformat, ";")

        if (!is.list(val)) val <- list(val)
        val <- lapply(
            val, function(x) paste0("\"", x, "\"", collapse=",")
        )

        qstring <- do.call(sprintf, args=c(qformat, val))

    } else {

        qstring <- qformat

    }

    dat <- suppressWarnings(gtoxQuery(query=qstring))

    if (nrow(dat) == 0) {
        warning("The given ", fld,"(s) are not in the gtox database.")
        return(dat)
    }

    dat[]

}

#-------------------------------------------------------------------------------