R/tcplMakeAeidPlts.R

In USEPA/CompTox-ToxCast-tcpl: ToxCast Data Analysis Pipeline

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

#' @title Create a .pdf with dose-response plots
#' 
#' @description
#' \code{tcplMakeAeidPlts} creates a .pdf file with the dose-response plots for 
#' the given aeid.
#' 
#' @param aeid Integer of length 1 or 2, the assay endpoint id
#' @param compare Boolean to for comparison of aeids if length(aeid)>1
#' @param lvl Integer of length 1, the data level to use (4-7). Only level 5-6 valid for compare aeids.
#' @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
#' @param cnst Constant hline to draw on plot
#' \code{\link{tcplLoadClib}} for more information. 
#' @inheritParams tcplPlotFits
#' 
#' @details 
#' \code{tcplMakeAeidPlts} provides a wrapper for \code{\link{tcplPlotFits}},
#' 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{tcplMakeAeidPlts}, but \code{FALSE} in \code{tcplPlotFits}
#' 
#' Note, only level 5 or level 6 is valid for comparing 2 aeids.
#' 
#' @examples
#' \dontrun{
#' ## Will produce the same result as the example for tcplPlotFits
#' tcplMakeAeidPlts(aeid = 1, lvl = 6, ordr.fitc = FALSE)
#' }
#' 
#' \dontrun{
#' ## Compare two aeids on same plots
#' tcplMakeAeidPlts(aeid = c(1,2), compare=T, lvl = 6)
#' }
#' 
#' @import data.table
#' @importFrom grDevices graphics.off pdf
#' @export

tcplMakeAeidPlts <- function(aeid, compare=F, lvl = 4L, fname = NULL, odir = getwd(), 
                             ordr.fitc = TRUE, clib = NULL, cnst=NULL) {
  
  ## Variable-binding to pass R CMD Check
  spid <- m4id <- NULL
  
  if (check_tcpl_db_schema()) stop("This function is no longer supported in this
                                   version of invitrodb. Consider tcplPlot() instead.")
  
  on.exit(graphics.off())
  
  if (length(aeid) > 2) stop("'aeid' must be of length 1 or 2.")
  if (length(lvl) > 1 | !lvl %in% 4:7) stop("Invalid 'lvl' input.")
  
  prs <- list(type = "mc", fld = "aeid", val = aeid)
  
  if (lvl < 5L) {
    dat <- do.call(tcplLoadData, args = c(lvl = 4L, prs))
  } else {
    dat <- do.call(tcplLoadData, args = c(lvl = 5L, prs))
  }
  
  if (nrow(dat) == 0) stop("No data for AEID", aeid)
  
  if (!is.null(clib)) {
    csub <- tcplLoadClib(field = "clib", val = clib)
    dat <- dat[spid %in% tcplLoadChem(field = "chid", val = csub$chid)$spid]
  }
  
  prs <- list(type = "mc", fld = "m4id", val = dat[ , unique(m4id)])
  
  agg <- do.call(tcplLoadData, args = c(lvl = "agg", prs))
  flg <- if (lvl < 6L) NULL else do.call(tcplLoadData, args = c(lvl = 6L, prs))
  boot <- if (lvl < 7L) NULL else do.call(tcplLoadData, args = c(lvl = 7L, prs))
  
  if (is.null(fname)) {
    if (!compare) {
      fname <- file.path(odir,
                         paste(paste0("AEID", aeid),
                               paste0("L", lvl),
                               tcplLoadAeid("aeid", aeid)$aenm,
                               format(Sys.Date(), "%y%m%d.pdf"),
                               sep = "_"))
    } else {
      tmp.aenm <- tcplLoadAeid("aeid", aeid)$aenm
      fname <- file.path(odir,
                         paste(sprintf("AEID%s_%s_VS_AEID%s_%s", aeid[1], tmp.aenm[1], aeid[2], tmp.aenm[2]),
                               paste0("L", lvl),
                               format(Sys.Date(), "%y%m%d.pdf"),
                               sep = "_"))
    }
  }
  
  graphics.off()
  pdf(file = fname, height = 6, width = 10, pointsize = 10)
  tcplPlotFits(dat = dat, agg = agg, flg = flg, boot = boot, ordr.fitc = ordr.fitc, cnst=cnst, orig.aeid=aeid, compare=compare)
  graphics.off()
  
  cat(fname, "complete.")
  
  TRUE
  
}

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