# Source code for cytoflowgui.view_plugins.stats_2d

```#!/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
# 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 Statistics Plot
------------------

Plot two statistics on a scatter plot.  A point (X,Y) is drawn for every
pair of elements with the same value of **Variable**; the X value is from
** X statistic** and the Y value is from **Y statistic**.

.. object:: X Statistic

Which statistic to plot on the X axis.

.. object:: Y Statistic

Which statistic to plot on the Y axis.  Must have the same indices as
**X Statistic**.

.. object:: X Scale, Y Scale

How to scale the X and Y axes.

.. object:: Variable

The statistic variable to put on the plot.

.. object:: Horizontal Facet

Make muliple plots, with each column representing a subset of the statistic
with a different value for this variable.

.. object:: Vertical Facet

Make multiple plots, with each row representing a subset of the statistic
with a different value for this variable.

.. object:: Color Facet

Make lines on the plot with different colors; each color represents a subset
of the statistic with a different value for this variable.

.. object:: Color Scale

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

.. object:: X Error Statistic

A statistic to use to make error bars in the X direction.  Must have the
same indices as the statistic in **X Statistic**.

.. object:: Y Error Statistic

A statistic to use to make error bars in the Y direction.  Must have the
same indices as the statistic in **Y Statistic**.

.. object:: Subset

Plot only a subset of the statistic.

.. 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()

ch_op = flow.ChannelStatisticOp(name = 'MeanByDox',
channel = 'Y2-A',
function = flow.geom_mean,
by = ['Dox'])
ex2 = ch_op.apply(ex)
ch_op_2 = flow.ChannelStatisticOp(name = 'SdByDox',
channel = 'Y2-A',
function = flow.geom_sd,
by = ['Dox'])
ex3 = ch_op_2.apply(ex2)

flow.Stats2DView(variable = 'Dox',
xstatistic = ('MeanByDox', 'geom_mean'),
xscale = 'log',
ystatistic = ('SdByDox', 'geom_sd'),
yscale = 'log').plot(ex3)
"""

import pandas as pd

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

import cytoflow.utility as util

from ..workflow.views import Stats2DWorkflowView, Stats2DPlotParams
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, Stats2DPlotParamsView

[docs]class Stats2DParamsHandler(Controller):
view_params_view = \
View(Item('linestyle'),
Item('marker'),
Item('markersize',
editor = TextEditor(auto_set = False),
format_func = lambda x: "" if x == None else str(x)),
Item('capsize',
editor = TextEditor(auto_set = False),
format_func = lambda x: "" if x == None else str(x)),
Item('alpha'),
Stats2DPlotParamsView.content)

[docs]class Stats2DHandler(ViewHandler):
indices = Property(depends_on = "context.statistics, model.xstatistic, model.ystatistic, model.subset")
numeric_indices = Property(depends_on = "context.statistics, model.xstatistic, model.ystatistic, model.subset")
levels = Property(depends_on = "context.statistics, model.xstatistic, model.ystatistic")

view_traits_view = \
View(VGroup(
VGroup(Item('xstatistic',
editor = EnumEditor(name = 'context_handler.numeric_statistics_names'),
label = "X Statistic"),
Item('xscale', label = "X Scale"),
Item('ystatistic',
editor = EnumEditor(name = 'context_handler.numeric_statistics_names'),
label = "Y Statistic"),
Item('yscale', label = "Y Scale"),
Item('variable',
editor=EnumEditor(name='handler.indices')),
Item('xfacet',
editor=ExtendableEnumEditor(name='handler.indices',
extra_items = {"None" : ""}),
label = "Horizontal\nFacet"),
Item('yfacet',
editor=ExtendableEnumEditor(name='handler.indices',
extra_items = {"None" : ""}),
label = "Vertical\nFacet"),
Item('huefacet',
editor=ExtendableEnumEditor(name='handler.indices',
extra_items = {"None" : ""}),
label="Color\nFacet"),
Item('huescale',
label = "Hue\nScale"),
Item('x_error_statistic',
editor=ExtendableEnumEditor(name='context_handler.statistics_names',
extra_items = {"None" : ("", "")}),
label = "X Error\nStatistic"),
Item('y_error_statistic',
editor=ExtendableEnumEditor(name='context_handler.statistics_names',
extra_items = {"None" : ("", "")}),
label = "Y Error\nStatistic"),
label = "Two-Dimensional Statistics Plot",
show_border = False),
VGroup(Item('subset_list',
show_label = False,
editor = SubsetListEditor(conditions = "handler.levels",
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 = Stats2DParamsHandler),
style = 'custom',
show_label = False))

# MAGIC: gets the value for the property indices
def _get_indices(self):
if not (self.context and self.context.statistics
and self.model.xstatistic in self.context.statistics
and self.model.ystatistic in self.context.statistics):
return []

xstat = self.context.statistics[self.model.xstatistic]
ystat = self.context.statistics[self.model.ystatistic]

try:
ystat.index = ystat.index.reorder_levels(xstat.index.names)
ystat.sort_index(inplace = True)
except AttributeError:
pass

index = xstat.index.intersection(ystat.index)

data = pd.DataFrame(index = index)

if self.model.subset:
data = data.query(self.model.subset)

if len(data) == 0:
return []

names = list(data.index.names)
for name in names:
unique_values = data.index.get_level_values(name).unique()
if len(unique_values) == 1:
data.index = data.index.droplevel(name)

return list(data.index.names)

# MAGIC: gets the value for the property numeric_indices
def _get_numeric_indices(self):
if not (self.context and self.context.statistics
and self.model.xstatistic in self.context.statistics
and self.model.ystatistic in self.context.statistics):
return []

xstat = self.context.statistics[self.model.xstatistic]
ystat = self.context.statistics[self.model.ystatistic]

try:
ystat.index = ystat.index.reorder_levels(xstat.index.names)
ystat.sort_index(inplace = True)
except AttributeError:
pass

index = xstat.index.intersection(ystat.index)
data = pd.DataFrame(index = index)

if self.model.subset:
data = data.query(self.model.subset)

if len(data) == 0:
return []

names = list(data.index.names)
for name in names:
unique_values = data.index.get_level_values(name).unique()
if len(unique_values) == 1:
data.index = data.index.droplevel(name)

data.reset_index(inplace = True)
return [x for x in data if util.is_numeric(data[x])]

# MAGIC: gets the value for the property 'levels'
# returns a Dict(Str, pd.Series)

def _get_levels(self):
if not (self.context and self.context.statistics
and self.model.xstatistic in self.context.statistics
and self.model.ystatistic in self.context.statistics):
return {}

xstat = self.context.statistics[self.model.xstatistic]
ystat = self.context.statistics[self.model.ystatistic]

index = xstat.index.intersection(ystat.index)

names = list(index.names)
for name in names:
unique_values = index.get_level_values(name).unique()
if len(unique_values) == 1:
index = index.droplevel(name)

names = list(index.names)
ret = {}
for name in names:
ret[name] = pd.Series(index.get_level_values(name)).sort_values()
ret[name] = pd.Series(ret[name].unique())

return ret

[docs]@provides(IViewPlugin)
class Stats2DPlugin(Plugin, PluginHelpMixin):

id = 'edu.mit.synbio.cytoflowgui.view.stats2d'
view_id = 'edu.mit.synbio.cytoflow.view.stats2d'
short_name = "2D Statistics View"

[docs]    def get_view(self):
return Stats2DWorkflowView()

[docs]    def get_handler(self, model, context):
if isinstance(model, Stats2DWorkflowView):
return Stats2DHandler(model = model, context = context)
elif isinstance(model, Stats2DPlotParams):
return Stats2DParamsHandler(model = model, context = context)

[docs]    def get_icon(self):
return ImageResource('stats_2d')

plugin = List(contributes_to = VIEW_PLUGIN_EXT)
def _plugin_default(self):
return [self]

```