Source code for cytoflowgui.view_plugins.violin

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

# (c) Massachusetts Institute of Technology 2015-2018
# (c) Brian Teague 2018-2022 2015-2017
# 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 <>.

Violin Plot

Plots a violin plot, which is a nice way to compare several distributions.

.. object:: X Variable

    The variable to compare on the X axis.

.. object:: Y Channel

    The channel to plot on the Y axis.
.. object:: Y Channel Scale

    How to scale the Y axis of the plot.
.. object:: Horizonal Facet

    Make multiple plots.  Each column has a unique value of this variable.
.. object:: Vertical Facet

    Make multiple plots.  Each row has a unique value of this variable.
.. object:: Color Facet

    Plot with multiple colors.  Each color has a unique value of this variable.
.. object:: Color Scale

    If **Color Facet** is a numeric variable, use this scale for the color
.. object:: Tab Facet

    Make multiple plots in differen tabs; each tab's plot has a unique value
    of this variable.
.. object:: Subset

    Plot only a subset of the data in the experiment.
.. 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()

    flow.ViolinPlotView(channel = 'Y2-A',
                        scale = 'log',
                        variable = 'Dox').plot(ex)

from traits.api import provides, List
from traitsui.api import View, Item, EnumEditor, VGroup, TextEditor, Controller
from envisage.api import Plugin
from pyface.api import ImageResource

from ..workflow.views import ViolinPlotWorkflowView, ViolinPlotParams
from ..editors import SubsetListEditor, ColorTextEditor, ExtendableEnumEditor, InstanceHandlerEditor
from ..subset_controllers import subset_handler_factory

from .i_view_plugin import IViewPlugin, VIEW_PLUGIN_EXT
from .view_plugin_base import ViewHandler, PluginHelpMixin, Data1DPlotParamsView

[docs]class ViolinParamsHandler(Controller): view_params_view = \ View(Item('bw', label = 'Bandwidth'), Item('scale_plot', label = "Plot scale"), Item('scale_hue'), Item('gridsize', editor = TextEditor(auto_set = False)), Item('inner'), Item('split'), Data1DPlotParamsView.content)
[docs]class ViolinHandler(ViewHandler): view_traits_view = \ View(VGroup( VGroup(Item('variable', editor=ExtendableEnumEditor(name='context_handler.conditions_names'), label = "X Variable"), Item('channel', editor=EnumEditor(name='context_handler.channels'), label = "Y Channel"), Item('scale', label = "Y Channel\nScale"), Item('xfacet', editor=ExtendableEnumEditor(name='context_handler.conditions_names', extra_items = {"None" : ""}), label = "Horizontal\nFacet"), Item('yfacet', editor=ExtendableEnumEditor(name='context_handler.conditions_names', extra_items = {"None" : ""}), label = "Vertical\nFacet"), Item('huefacet', editor=ExtendableEnumEditor(name='context_handler.conditions_names', extra_items = {"None" : ""}), label="Color\nFacet"), Item('huescale', label = "Color\nScale"), Item('plotfacet', editor=ExtendableEnumEditor(name='context_handler.conditions_names', extra_items = {"None" : ""}), label = "Tab\nFacet"), label = "Violin Plot", show_border = False), VGroup(Item('subset_list', show_label = False, editor = SubsetListEditor(conditions = "context_handler.conditions", editor = InstanceHandlerEditor(view = 'subset_view', handler_factory = subset_handler_factory), mutable = False)), label = "Subset", show_border = False, show_labels = 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 = ViolinParamsHandler), style = 'custom', show_label = False))
[docs]@provides(IViewPlugin) class ViolinPlotPlugin(Plugin, PluginHelpMixin): id = '' view_id = '' short_name = "Violin Plot"
[docs] def get_view(self): return ViolinPlotWorkflowView()
[docs] def get_handler(self, model, context): if isinstance(model, ViolinPlotWorkflowView): return ViolinHandler(model = model, context = context) elif isinstance(model, ViolinPlotParams): return ViolinParamsHandler(model = model, context = context)
[docs] def get_icon(self): return ImageResource('violin')
plugin = List(contributes_to = VIEW_PLUGIN_EXT) def _plugin_default(self): return [self]