R/writeIFC.R

In gitdemont/IFC: Tools for Imaging Flow Cytometry

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# This file is released under the GNU General Public License, Version 3, GPL-3 #
# Copyright (C) 2020 Yohann Demont                                             #
#                                                                              #
# It is part of IFC package, please cite:                                      #
# -IFC: An R Package for Imaging Flow Cytometry                                #
# -YEAR: 2020                                                                  #
# -COPYRIGHT HOLDERS: Yohann Demont, Gautier Stoll, Guido Kroemer,             #
#                     Jean-Pierre Marolleau, Loïc Garçon,                      #
#                     INSERM, UPD, CHU Amiens                                  #
#                                                                              #
# DISCLAIMER:                                                                  #
# -You are using this package on your own risk!                                #
# -We do not guarantee privacy nor confidentiality.                            #
# -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. In no event shall the copyright holders or #
# contributors be liable for any direct, indirect, incidental, special,        #
# exemplary, or consequential damages (including, but not limited to,          #
# procurement of substitute goods or services; loss of use, data, or profits;  #
# or business interruption) however caused and on any theory of liability,     #
# whether in contract, strict liability, or tort (including negligence or      #
# otherwise) arising in any way out of the use of this software, even if       #
# advised of the possibility of such damage.                                   #
#                                                                              #
# You should have received a copy of the GNU General Public License            #
# along with IFC. If not, see <http://www.gnu.org/licenses/>.                  #
################################################################################

#' @title IFC Files Generic Writer
#' @description
#' Writes IFC data to DAF and subsets or merges RIF/CIF Files.
#' @param fileName path to file.
#' @param ... arguments to pass to \code{\link{ExportToDAF}}, \code{\link{ExportToXIF}}, \code{\link{ExportToFCS}}, or \code{\link{data_to_DAF}}.
#' @details If an `IFC_data` object is provided as 'fileName' or in '...' \code{\link{ExportToFCS}} or \code{\link{data_to_DAF}} will be used to export object.
#' Otherwise, if 'fileName' is a DAF file \code{\link{ExportToDAF}} will be used to write file whereas if it is RIF or CIF file(s) \code{\link{writeIFC}} will use \code{\link{ExportToXIF}}.
#' @return it invisible returns the path of exported file.
#' @examples
#' if(requireNamespace("IFCdata", quietly = TRUE)) {
#'   tmp <- tempdir(check = TRUE)
#'   ## use a daf file
#'   file_daf <- system.file("extdata", "example.daf", package = "IFCdata")
#'   ## create a tagged population named test with 1st object
#'   pop <- buildPopulation(name = "test", type = "T", obj = 0)
#'   writeIFC(file_daf, write_to = paste0(tmp, "\\test_write.daf"),
#'            overwrite = TRUE, pops = list(pop))
#'   ## use a rif file, but you can also use a cif
#'   file_rif <- system.file("extdata", "example.rif", package = "IFCdata")
#'   writeIFC(fileName = file_rif, write_to = paste0(tmp, "\\test_write.rif"), 
#'            overwrite = TRUE, objects = 0)
#' } else {
#'   message(sprintf('Please run `install.packages("IFCdata", repos = "%s", type = "source")` %s',
#'                   'https://gitdemont.github.io/IFCdata/',
#'                   'to install extra files required to run this example.'))
#' }
#' @export
writeIFC <- function(fileName, ...) {
  dots=list(...)
  input = whoami(entries=as.list(match.call()), search=list(obj = "IFC_data"))
  fileName = input$fileName
  write_to = dots$write_to
  if(length(write_to) == 0) stop("'write_to' can't be missing")
  splitp_obj <- splitp(write_to)
  splitf_obj <- splitf(ifelse(length(input$obj) == 0, normalizePath(fileName[1], winslash="/", mustWork=TRUE), input$obj$fileName))
  file_extension <- getFileExt(formatn(splitp_obj, splitf_obj))
  if(length(input$obj) == 0) {
    assert(file_extension, alw = c("daf","rif","cif"))
    if(file_extension == "daf") return(ExportToDAF(fileName=fileName, ...))
    return(ExportToXIF(fileName=fileName, ...)) 
  } else {
    to_remove <- (attr(input,"was")[(attr(input,"was")>1)] - as.integer(length(fileName) != 0))
    to_remove <- c(to_remove, na.omit(which(names(dots) == "obj")))
    if(length(to_remove) != 0) dots=dots[-to_remove]
    assert(file_extension, alw = c("daf","fcs"))
    if(file_extension == "daf") return(do.call(what=data_to_DAF, args=c(dots, list(obj=quote(input$obj)))))
    return(do.call(what=ExportToFCS, args=c(dots, list(obj=quote(input$obj)))))
  }
}