Source code for cytoflowgui.view_plugins.scatterplot

#!/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 <>.


Plot a scatterplot.

.. 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
.. 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.ScatterplotView(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

from ..workflow.views import ScatterplotWorkflowView, ScatterplotPlotParams
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 ScatterplotParamsHandler(Controller): view_params_view = \ View(Item('alpha', editor = TextEditor(auto_set = False)), Item('s', editor = TextEditor(auto_set = False), label = "Size"), Item('marker'), Data2DPlotParamsView.content)
[docs]class ScatterplotHandler(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 = "Scatter 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 = ScatterplotParamsHandler), style = 'custom', show_label = False))
[docs]@provides(IViewPlugin) class ScatterplotPlugin(Plugin, PluginHelpMixin): id = '' view_id = '' short_name = "Scatter Plot"
[docs] def get_view(self): return ScatterplotWorkflowView()
[docs] def get_handler(self, model, context): if isinstance(model, ScatterplotWorkflowView): return ScatterplotHandler(model = model, context = context) elif isinstance(model, ScatterplotPlotParams): return ScatterplotParamsHandler(model = model, context = context)
[docs] def get_icon(self): return ImageResource('scatterplot')
plugin = List(contributes_to = VIEW_PLUGIN_EXT) def _plugin_default(self): return [self]