ExportToDAF: DAF File Writer

In IFC: Tools for Imaging Flow Cytometry

DAF File Writer

Description

Writes a new DAF file based on another one and exports new region(s), pop(s), feature(s), graph(s) and / or mask(s).

Usage

ExportToDAF(
  fileName,
  write_to,
  pops = list(),
  regions = list(),
  features = list(),
  graphs = list(),
  masks = list(),
  viewing_pop = "All",
  endianness = .Platform$endian,
  verbose = FALSE,
  overwrite = FALSE,
  fullname = TRUE,
  cifdir = dirname(fileName),
  ntry = +Inf,
  ...
)

Arguments

fileName	path of file to read data from.
write_to	pattern used to export file. Placeholders, like "%d/%s_fromR.%e", will be substituted: -%d: with full path directory of 'fileName' -%p: with first parent directory of 'fileName' -%e: with extension of 'fileName' (without leading .) -%s: with shortname from 'fileName' (i.e. basename without extension). Exported file extension will be deduced from this pattern. Note that has to be a .daf.
pops	list of population(s) to export. Will be coerced to exportable format by buildPopulation.
regions	list of region(s) to export. Will be coerced to exportable format by buildRegion.
features	list of feature(s) to export.
graphs	list of graph(s) to export. Not yet implemented.
masks	list of mask(s) to export. Not yet implemented.
viewing_pop	Character String. Allow user to change displayed population. Default is 'All'.
endianness	The endian-ness ("big" or "little") of the target system for the file. Default is .Platform$endian. Endianness describes the bytes order of data stored within the files. This parameter may not be modified.
verbose	whether to display information (use for debugging purpose). Default is FALSE.
overwrite	whether to overwrite file or not. Default is FALSE. Note that if TRUE, it will overwrite exported file if path of 'fileName' and deduced from 'write_to' arguments are different. Otherwise, you will get an error saying that overwriting source file is not allowed. Note also that an original file, i.e. generated by IDEAS(R) or INSPIRE(R), will never be overwritten. Otherwise, you will get an error saying that overwriting original file is not allowed.
fullname	whether to export daf file with full name of its corresponding cif, if found. Default is TRUE. If cif can't be found, daf file will be exported with the original cif file name.
cifdir	the path of the directory to initially look to cif file. Default is dirname(fileName). Only apply when 'fullname' is set to TRUE.
ntry	number of times ExportToDAF will be allowed to find corresponding cif file. Default is +Inf. Only apply when 'fullname' is set to TRUE.
...	other arguments to be passed.

Value

It invisibly returns full path of exported file.

Examples

if(requireNamespace("IFCdata", quietly = TRUE)) {
  ## use a daf file
  file_daf <- system.file("extdata", "example.daf", package = "IFCdata")
  tmp <- tempdir(check = TRUE)
  ## create a tagged population named test with 1st object
  pop <- buildPopulation(name = "test", type = "T", obj = 0)
  ExportToDAF(file_daf, write_to = paste0(tmp, "\\test.daf"),
              overwrite = TRUE, pops = list(pop))
} 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.'))
}

IFC documentation built on Sept. 14, 2023, 1:08 a.m.