Source code for cytoflowgui.op_plugins.density

#!/usr/bin/env python3.8
# coding: latin-1

# (c) Massachusetts Institute of Technology 2015-2018
# (c) Brian Teague 2018-2022
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <>.

Density Gate

Computes a gate based on a 2D density plot.  The user chooses what proportion
of events to keep, and the module creates a gate that selects those events in
the highest-density bins of a 2D density histogram.
A single gate may not be appropriate for an entire experiment.  If this is the 
case, you can use **By** to specify metadata by which to aggregate the data 
before computing and applying the gate.  
.. object:: Name
    The operation name; determines the name of the new metadata
.. object:: X Channel, Y Channel
    The channels to apply the mixture model to.

.. object:: X Scale, Y Scale 

    Re-scale the data in **Channel** before fitting. 

.. object:: Keep

    The proportion of events to keep in the gate.  Defaults to 0.9.
.. object:: By 

    A list of metadata attributes to aggregate the data before estimating
    the model.  For example, if the experiment has two pieces of metadata,
    ``Time`` and ``Dox``, setting **by** to ``["Time", "Dox"]`` will fit 
    the model separately to each subset of the data with a unique combination of
    ``Time`` and ``Dox``.

.. plot::
   :include-source: False

    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()

    density_op = flow.DensityGateOp(name = 'Density',
                                    xchannel = 'FSC-A',
                                    xscale = 'log',
                                    ychannel = 'SSC-A',
                                    yscale = 'log',
                                    keep = 0.5)
    ex2 = density_op.apply(ex)

from traits.api import provides, List
from traitsui.api import (View, Item, EnumEditor, VGroup, TextEditor, 
                          CheckListEditor, ButtonEditor)
from envisage.api import Plugin
from pyface.api import ImageResource

from ..view_plugins import ViewHandler
from ..view_plugins.density import DensityParamsHandler
from ..editors import SubsetListEditor, ColorTextEditor, InstanceHandlerEditor
from ..workflow.operations import DensityGateWorkflowOp, DensityGateWorkflowView
from ..subset_controllers import subset_handler_factory

from .i_op_plugin import IOperationPlugin, OP_PLUGIN_EXT
from .op_plugin_base import OpHandler, shared_op_traits_view, PluginHelpMixin

[docs]class DensityGateHandler(OpHandler): operation_traits_view = \ View(Item('name', editor = TextEditor(auto_set = False, placeholder = "None")), Item('xchannel', editor=EnumEditor(name='context_handler.previous_channels'), label = "X Channel"), Item('ychannel', editor=EnumEditor(name='context_handler.previous_channels'), label = "Y Channel"), Item('xscale', label = "X Scale"), Item('yscale', label = "Y Scale"), VGroup( Item('keep', editor = TextEditor(auto_set = False, evaluate = float, format_func = lambda x: "" if x is None else str(x), placeholder = "None"), label = "Proportion\nto keep"), Item('by', editor = CheckListEditor(cols = 2, name = 'context_handler.previous_conditions_names'), label = 'Group\nEstimates\nBy', style = 'custom'), VGroup(Item('subset_list', show_label = False, editor = SubsetListEditor(conditions = "context_handler.previous_conditions", editor = InstanceHandlerEditor(view = 'subset_view', handler_factory = subset_handler_factory))), label = "Subset", show_border = False, show_labels = False), Item('do_estimate', editor = ButtonEditor(value = True, label = "Estimate!"), show_label = False), label = "Estimation parameters", show_border = False), shared_op_traits_view)
[docs]class DensityGateViewHandler(ViewHandler): view_traits_view = \ View(VGroup( VGroup(Item('xchannel', label = "X channel", style = 'readonly'), Item('ychannel', label = "Y channel", style = 'readonly'), Item('xscale', label = "X scale", style = 'readonly'), Item('yscale', label = "Y scale", style = 'readonly'), Item('huescale', label = "Hue scale"), label = "Density Gate Default Plot", show_border = False)), Item('context.view_warning', resizable = True, visible_when = 'context.view_warning', editor = ColorTextEditor(foreground_color = "#000000", background_color = "#ffff99")), Item('context.view_error', resizable = True, visible_when = 'context.view_error', editor = ColorTextEditor(foreground_color = "#000000", background_color = "#ff9191"))) view_params_view = \ View(Item('plot_params', editor = InstanceHandlerEditor(view = 'view_params_view', handler_factory = DensityParamsHandler), style = 'custom', show_label = False))
[docs]@provides(IOperationPlugin) class DensityGatePlugin(Plugin, PluginHelpMixin): id = '' operation_id = '' view_id = '' short_name = "Density Gate" menu_group = "Gates"
[docs] def get_operation(self): return DensityGateWorkflowOp()
[docs] def get_handler(self, model, context): if isinstance(model, DensityGateWorkflowOp): return DensityGateHandler(model = model, context = context) elif isinstance(model, DensityGateWorkflowView): return DensityGateViewHandler(model = model, context = context)
[docs] def get_icon(self): return ImageResource('density')
plugin = List(contributes_to = OP_PLUGIN_EXT) def _plugin_default(self): return [self]