#!/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
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# 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 <http://www.gnu.org/licenses/>.
"""
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
bar.
.. 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 # @UnresolvedImport
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 = 'cytoflowgui.view_plugins.violin'
view_id = 'cytoflow.view.violin'
name = "Violin Plot"
short_name = "Violin"
[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]