R/gtoxPlotFits.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.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# gtoxPlotFits: Plot fits based on mc4/5 and mc4_agg
#-------------------------------------------------------------------------------

#' @title Plot summary fits based on fit and dose-response data
#'
#' @description
#' \code{gtoxPlotFits} takes the dose-response and fit data and produces
#' summary plot figures.
#'
#' @param dat data.table, level 4 or level 5 data, see details.
#' @param agg data.table, concentration-response aggregate data, see details.
#' @param flg data.table, level 6 data, see details.
#' @param ordr.fitc Logical, should the fits be ordered by fit category?
#' @param bline Character of length 1, the value used for drawing the baseline
#' noise
#'
#' @details
#' The data for 'dat', 'agg', and 'flg' should be loaded using the
#' \code{\link{gtoxLoadData}} function with the appropriate 'lvl' parameter.
#' See help page for \code{gtoxLoadData} for more information.
#'
#' Supplying level 4 data for the 'dat' parameter will result in level 4 plots.
#' Similarly, supp
#'
#' If fits are not ordered by fit category, they will be ordered by chemical
#' ID. Inputs with multiple assay endpoints will first be ordered by assay
#' endpoint ID.
#'
#' Any values for 'bline' other than 'coff' will use 3*bmad.
#'
#' @examples
#'
#' ## Store the current config settings, so they can be reloaded at the end
#' ## of the examples
#' conf_store <- gtoxConfList()
#' gtoxConfDefault()
#'
#' ## gtoxPlotFits needs data.tables supplying the concentration/response
#' ## data stored in mc4_agg, as well as the fit information from mc4 or mc5.
#' ## Additionally, gtoxPlotFits will take level 6 data from mc6 and add the
#' ## flag information to the plots. The following shows how to make level 6
#' ## plots. Omitting the 'flg' parameter would result in level 5 plots, and
#' ## loading level 4, rather than level 5 data, would result in level 4 plots.
#' 
#' aeid = 2
#' l5 <- gtoxLoadData(lvl = 5, fld = "aeid", val = aeid)
#' l4_agg <- gtoxLoadData(lvl = "agg", fld = "aeid", val = aeid)
#' l6 <- gtoxLoadData(lvl = 6, fld = "aeid", val = aeid)
#' \dontrun{
#' pdf(file = "gtoxPlotFits.pdf", height = 6, width = 10, pointsize = 10)
#' gtoxPlotFits(dat = l5, agg = l4_agg, flg = l6)
#' graphics.off()
#' }
#'
#' ## While it is most likely the user will want to just save all of the plots
#' ## to view in a PDF, the 'browse' parameter can be used to quickly view
#' ## some plots.
#'
#' ## Start by identifying some sample IDs to plot, then call gtoxPlotFits with
#' ## a subset of the data. This browse function is admittedly clunky.
#' bpa <- gtoxLoadChem(field = "chnm", val = "chromium")[ , spid]
#' l5_sub <- l5[spid %in% bpa]
#' 
#' gtoxPlotFits(dat = l5_sub, agg = l4_agg[m4id %in% l5_sub$m4id])
#' 
#'
#' ## Reset configuration
#' options(conf_store)
#' 
#' @return None
#'
#' @import data.table
#' @export

gtoxPlotFits <- function(dat, agg, flg=NULL, ordr.fitc=FALSE, bline="bmad") {

    ## Variable-binding to pass R CMD Check
    chid <- chnm <- spid <- aenm <- aeid <- m4id <- fitc <- fval <- NULL
    flgo <- mc6_mthd_id <- J <- NULL

    if (!is.null(flg) & !"m5id" %in% names(dat)) {
        stop("Must supply level 5 data with a non-null 'flg' input.")
    }

    dat <- gtoxPrepOtpt(dat)
    dat[is.na(chid), chnm := paste(spid, "(spid not in DB)")]
    dat[ , aenm := paste0("AEID", aeid, " (", aenm, ")")]

    setkey(dat, m4id)
    setkey(agg, m4id)

    ## Set the plotting order
    if (ordr.fitc && "fitc" %in% names(dat)) {
        m4ids <- dat[order(aeid, fitc, chid), unique(m4id)]
    } else {
        m4ids <- dat[order(aeid, chid), unique(m4id)]
    }

    if (!is.null(flg)) {
        if (nrow(flg) > 0) {
            flg[is.na(fval),  flgo := as.character(mc6_mthd_id)]
            flg[!is.na(fval),
                flgo := paste0(mc6_mthd_id, " (", signif(fval, 3), ")")]
            flg <- flg[ ,
                list(flgo=paste(unique(flgo), collapse="; ")),
                by=m4id]
            setkey(flg, m4id)
            dat <- flg[dat]
        } else {
            dat[ , flgo := NA]
        }
    }

    for (i in m4ids) {

        resp <- agg[J(i), resp]
        logc <- agg[J(i), logc]
        pars <- as.list(dat[J(i)])
        .plotFit(resp=resp, logc=logc, pars=pars, bline=bline)

    }

}

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