#!/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 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:: Statistic
Which statistic to plot.
.. object:: X Feature
Which feature to plot on the X axis.
.. object:: Y Feature
Which feature to plot on the Y axis.
.. 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 pandas as pd
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 = lambda x: pd.Series({'Geo.Mean' : flow.geom_mean(x),
'Geo.SD' : flow.geom_sd(x)}),
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',
statistic = 'MeanByDox',
xfeature = 'Geo.Mean',
xscale = 'log',
yfeature = 'Geo.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 # @UnresolvedImport
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.statistic, model.subset")
numeric_indices = Property(depends_on = "context.statistics, model.statistic, model.subset")
levels = Property(depends_on = "context.statistics, model.statistic")
features = Property(depends_on = "context.statistics, model.statistic")
view_traits_view = \
View(VGroup(
VGroup(Item('statistic',
editor = EnumEditor(name = 'context_handler.statistics_names'),
label = "Statistic"),
Item('xfeature',
editor = EnumEditor(name='handler.features'),
label = "X Feature"),
Item('xscale', label = "X Scale"),
Item('yfeature',
editor = EnumEditor(name = 'handler.features'),
label = "Y Feature"),
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('xerror_low',
editor=ExtendableEnumEditor(name='handler.features',
extra_items = {"None" : ("", "")}),
label = "X Error\nStatistic (Low)"),
Item('xerror_high',
editor=ExtendableEnumEditor(name='handler.features',
extra_items = {"None" : ("", "")}),
label = "X Error\nStatistic (High)"),
Item('yerror_low',
editor=ExtendableEnumEditor(name='handler.features',
extra_items = {"None" : ("", "")}),
label = "Y Error\nStatistic (Low)"),
Item('yerror_high',
editor=ExtendableEnumEditor(name='handler.features',
extra_items = {"None" : ("", "")}),
label = "Y Error\nStatistic (High)"),
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.statistic in self.context.statistics):
return []
stat = self.context.statistics[self.model.statistic]
data = pd.DataFrame(index = stat.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 'levels'
# returns a Dict(Str, pd.Series)
def _get_levels(self):
if not (self.context and self.context.statistics
and self.model.statistic in self.context.statistics):
return {}
stat = self.context.statistics[self.model.statistic]
index = stat.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
# 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.statistic in self.context.statistics):
return []
stat = self.context.statistics[self.model.statistic]
data = pd.DataFrame(index = stat.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 "features"
def _get_features(self):
if not (self.context and self.context.statistics
and self.model.statistic in self.context.statistics):
return []
stat = self.context.statistics[self.model.statistic]
return stat.columns.to_list()
[docs]
@provides(IViewPlugin)
class Stats2DPlugin(Plugin, PluginHelpMixin):
id = 'cytoflowgui.view.stats2d'
view_id = 'cytoflow.view.stats2d'
name = "2D Statistics View"
short_name = "Stats 2D"
[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]