writeGatingStrategy: Gating Strategy File Writer

Description

Writes GatingML from an `IFC_data` object to a xml file

Usage

writeGatingStrategy(
  obj,
  write_to,
  overwrite = FALSE,
  display_progress = TRUE,
  verbose = FALSE,
  ...
)

Value

It invisibly returns full path of exported file.

Arguments

obj: an `IFC_data` object extracted with features extracted.
write_to: pattern used to export file. Placeholders, like "%d/%s_fromR.%e", will be substituted:
-%d: with full path directory of 'obj$fileName'
-%p: with first parent directory of 'obj$fileName'
-%e: with extension of 'obj$fileName' (without leading .)
-%s: with shortname from 'obj$fileName' (i.e. basename without extension).
Exported file extension will be deduced from this pattern. Note that it has to be a .xml.
overwrite: whether to overwrite file or not. Default is FALSE.
display_progress: whether to display a progress bar. Default is TRUE.
verbose: whether to display information (use for debugging purpose). Default is FALSE.
...: other arguments to be passed.

Details

Partial implementation of ISAC's Gating-ML 2.0 data exchange standard for gating description. See Josef Spidlen et al. Cytometry A 87 683-687 (2015). tools:::Rd_expr_doi("10.1002/cyto.a.22690")
GatingML is partly implemented because:
-Tagged population are not part of GatingML gates
-IDEAS/INSPIRE regions are different from the collection of gates listed in GatingML. Notably,
--only 1 or 2 dimensions gates will be used, --range gates and quadrant gates are absent from IDEAS/INSPIRE --ellipse gates exist in IDEAS/INSPIRE but are axis aligned and not rotated. -Transformation applied in IFC is not part of GatingML. Nonetheless, when possible additional information are provided in dedicated custom_info field.