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, use enum_files to figure out which files will be created from a particular experiment, and export 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)

subset

A Python expression used to select a subset of the data

Type

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