Writes GatingML from an `IFC_data` object to a xml file
writeGatingStrategy(
obj,
write_to,
overwrite = FALSE,
display_progress = TRUE,
verbose = FALSE,
...
)an `IFC_data` object extracted with features extracted.
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.
whether to overwrite file or not. Default is FALSE.
whether to display a progress bar. Default is TRUE.
whether to display information (use for debugging purpose). Default is FALSE.
other arguments to be passed.
It invisibly returns full path of exported file.
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). https://onlinelibrary.wiley.com/doi/full/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.