#!/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
# 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/>.
"""
2D Kernel Density Estimate
--------------------------
Plots a 2-d kernel-density estimate. Sort of like a smoothed histogram.
The density is visualized with a set of isolines.
.. object:: X Channel, Y Channel
The channels to plot on the X and Y axes.
.. object:: X Scale, Y Scale
How to scale the X and Y axes 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.Kde2DView(xchannel = 'V2-A',
xscale = 'log',
ychannel = 'Y2-A',
yscale = 'log',
huefacet = '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 Kde2DWorkflowView, Kde2DPlotParams
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, Data2DPlotParamsView
[docs]
class Kde2DParamsHandler(Controller):
view_params_view = \
View(Item('shade'),
Item('min_alpha',
editor = TextEditor(auto_set = False)),
Item('max_alpha',
editor = TextEditor(auto_set = False)),
Item('n_levels',
editor = TextEditor(auto_set = False),
label = "Num\nlevels"),
Item('bw', label = "Bandwidth"),
Item('gridsize',
editor = TextEditor(auto_set = False),
label = "Grid size"),
Data2DPlotParamsView.content)
[docs]
class Kde2DHandler(ViewHandler):
view_traits_view = \
View(VGroup(
VGroup(Item('xchannel',
editor=EnumEditor(name='context_handler.channels'),
label = "X Channel"),
Item('xscale',
label = "X Scale"),
Item('ychannel',
editor=EnumEditor(name='context_handler.channels'),
label = "Y Channel"),
Item('yscale',
label = "Y Scale"),
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 = "2D Kernel Density Estimate",
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 = Kde2DParamsHandler),
style = 'custom',
show_label = False))
[docs]
@provides(IViewPlugin)
class Kde2DPlugin(Plugin, PluginHelpMixin):
id = 'cytoflowgui.view.kde2d'
view_id = 'cytoflow.view.kde2d'
name = "2D Kernel Density Estimate"
short_name = "2D KDE"
[docs]
def get_view(self):
return Kde2DWorkflowView()
[docs]
def get_handler(self, model, context):
if isinstance(model, Kde2DWorkflowView):
return Kde2DHandler(model = model, context = context)
elif isinstance(model, Kde2DPlotParams):
return Kde2DParamsHandler(model = model, context = context)
[docs]
def get_icon(self):
return ImageResource('kde_2d')
plugin = List(contributes_to = VIEW_PLUGIN_EXT)
def _plugin_default(self):
return [self]