cytoflow.views.export_fcs¶
A “view” that exports events as FCS files.
ExportFCS
– the IView
class that does the exporting.
- class cytoflow.views.export_fcs.ExportFCS[source]¶
Bases:
traits.has_traits.HasStrictTraits
Exports events as FCS files.
This isn’t a traditional view, in that it doesn’t implement
plot
. Instead, useenum_files
to figure out which files will be created from a particular experiment, andexport
to export the FCS files.The Cytoflow attributes will be encoded in keywords in the FCS TEXT segment, starting with the characters
CF_
. Any FCS keywords that are the same across all the input files will also be included.- base¶
The prefix of the FCS filenames
- Type
Str
- path¶
The directory to export to.
- Type
Directory
- by¶
A list of conditions from
Experiment.conditions
; each unique combination of conditions will be exported to an FCS file.- Type
List(Str)
- keywords¶
If you want to add more keywords to the FCS files’ TEXT segment, specify them here.
- Type
Dict(Str, Str)
Examples
Make a little data set.
>>> import cytoflow as flow >>> import_op = flow.ImportOp() >>> import_op.tubes = [flow.Tube(file = "Plate01/RFP_Well_A3.fcs", ... conditions = {'Dox' : 10.0}), ... flow.Tube(file = "Plate01/CFP_Well_A4.fcs", ... conditions = {'Dox' : 1.0})] >>> import_op.conditions = {'Dox' : 'float'} >>> ex = import_op.apply()
Export the data
>>> import tempfile >>> flow.ExportFCS(path = 'export/', ... by = ["Dox"], ... subset = "Dox == 10.0").export(ex)
- enum_files(experiment)[source]¶
Return an iterator over the file names that this export module will produce from a given experiment.
- Parameters
experiment (Experiment) – The
Experiment
to export
- export(experiment)[source]¶
Export FCS files from an experiment.
- Parameters
experiment (Experiment) – The
Experiment
to export