R/gtoxMakeAeidPlts.R

In pmpsa-hpc/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.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# gtoxMakeAeidPlts: Create a .pdf with dose-response plots
#-------------------------------------------------------------------------------

#' @title Create a .pdf with dose-response plots
#'
#' @description
#' \code{gtoxMakeAeidPlts} creates a .pdf file with the dose-response plots for
#' the given aeid.
#'
#' @param aeid Integer of length 1, the assay endpoint id
#' @param lvl Integer of lengh 1, the data level to use (4-6)
#' @param fname Character, the filename
#' @param odir The directory to save the .pdf file in
#' @param clib Character, the chemical library to subset on, see
#' \code{\link{gtoxLoadClib}} for more information.
#' @inheritParams gtoxPlotFits
#'
#' @details
#' \code{gtoxMakeAeidPlts} provides a wrapper for \code{\link{gtoxPlotFits}},
#' allowing the user to produce PDFs with the curve plots without having to
#' separately load all of the data and establish the PDF device.
#'
#' If 'fname' is \code{NULL}, a default name is given by concatenating together
#' assay information.
#'
#' Note, the default value for ordr.fitc is \code{TRUE} in
#' \code{gtoxMakeAeidPlts}, but \code{FALSE} in \code{gtoxPlotFits}
#'
#' @examples
#' ## Save Aeid plot in a pdf file
#' gtoxMakeAeidPlts(aeid = 10, lvl = 6, ordr.fitc = FALSE)
#' 
#' @return None
#'
#' @import data.table
#' @importFrom grDevices graphics.off pdf
#' @export

gtoxMakeAeidPlts <- function(aeid, lvl=4L, fname=NULL, odir=getwd(),
    ordr.fitc=TRUE, clib=NULL) {

    ## Variable-binding to pass R CMD Check
    spid <- m4id <- NULL

    on.exit(graphics.off())

    if (length(aeid) > 1) stop("'aeid' must be of length 1.")
    if (length(lvl) > 1 | !lvl %in% 4:6) stop("Invalid 'lvl' input.")

    prs <- list(type="mc", fld="aeid", val=aeid)

    if (lvl < 5L) {
        dat <- do.call(gtoxLoadData, args=c(lvl=4L, prs))
    } else {
        dat <- do.call(gtoxLoadData, args=c(lvl=5L, prs))
    }

    if (nrow(dat) == 0) stop("No data for AEID", aeid)

    if (!is.null(clib)) {
        csub <- gtoxLoadClib(field="clib", val=clib)
        dat <- dat[spid %in% gtoxLoadChem(field="chid", val=csub$chid)$spid]
    }

    prs <- list(type="mc", fld="m4id", val=dat[ , unique(m4id)])

    agg <- do.call(gtoxLoadData, args=c(lvl="agg", prs))
    flg <- if (lvl < 6L) {
            NULL
        } else {
            do.call(
                gtoxLoadData,
                args=c(lvl=6L, prs)
            )
        }

    if (is.null(fname)) {
        fname <- file.path(
            odir,
            paste(
                paste0("AEID", aeid),
                paste0("L", lvl),
                gtoxLoadAeid("aeid", aeid)$aenm,
                format(Sys.Date(), "%y%m%d.pdf"),
                sep="_"
            )
        )
    }

    graphics.off()
    pdf(file=fname, height=6, width=10, pointsize=10)
    gtoxPlotFits(dat, agg, flg, ordr.fitc=ordr.fitc)
    graphics.off()

    cat(fname, "complete.")

    TRUE

}

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