#!/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/>.
"""
Bar Chart
---------
Plots a bar chart of a statistic.
Each variable in the statistic (ie, each variable chosen in the statistic
operation's **Group By**) must be set as **Variable** or as a facet.
.. object:: Statistic
Which statistic to plot. This is usually the name of the operation that
added the statistic.
.. object:: Feature
Which column in the statistic should be plotted?
.. object:: Variable
The statistic variable to use as the major bar groups.
.. object:: Scale
How to scale the statistic 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:: Hue Facet
Make multiple bars with different colors; each color represents a subset
of the statistic with a different value for this variable.
.. object:: Error Statistic
A statistic to use to make the error bars. Must have the same variables
as the statistic in **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()
ex2 = flow.ThresholdOp(name = 'Threshold',
channel = 'Y2-A',
threshold = 2000).apply(ex)
ex3 = flow.ChannelStatisticOp(name = "ByDox",
channel = "Y2-A",
by = ['Dox', 'Threshold'],
function = len).apply(ex2)
flow.BarChartView(statistic = "ByDox",
feature = "Y2-A",
variable = "Dox",
huefacet = "Threshold").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
from ..workflow.views import BarChartWorkflowView, BarChartPlotParams
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, Stats1DPlotParamsView
[docs]
class BarChartParamsHandler(Controller):
view_params_view = \
View(Item('errwidth',
editor = TextEditor(auto_set = False,
format_func = lambda x: "" if x == None else str(x)),
label = "Error bar\nwidth"),
Item('capsize',
editor = TextEditor(auto_set = False,
format_func = lambda x: "" if x == None else str(x)),
label = "Cap width"),
Stats1DPlotParamsView.content)
[docs]
class BarChartHandler(ViewHandler):
features = Property(depends_on = "context.statistics, model.statistic")
indices = Property(depends_on = "context.statistics, model.statistic, model.subset")
levels = 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('feature',
editor = EnumEditor(name = 'handler.features'),
label = "Feature"),
Item('variable',
editor=EnumEditor(name='handler.indices'),
label = "Variable"),
Item('scale', label = "Scale"),
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="Hue\nFacet"),
Item('error_low',
editor=ExtendableEnumEditor(name='handler.features',
extra_items = {"None" : ""}),
label = "Error Bar Low"),
Item('error_high',
editor=ExtendableEnumEditor(name='handler.features',
extra_items = {"None" : ""}),
label = "Error Bar High"),
label = "Bar Chart",
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 = BarChartParamsHandler),
style = 'custom',
show_label = False))
# 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()
# 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]
if self.model.subset:
stat = stat.query(self.model.subset)
if len(stat) == 0:
return []
names = list(stat.index.names)
for name in names:
unique_values = stat.index.get_level_values(name).unique()
if len(unique_values) == 1:
stat.index = stat.index.droplevel(name)
return list(stat.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
[docs]
@provides(IViewPlugin)
class BarChartPlugin(Plugin, PluginHelpMixin):
id = 'cytoflowgui.view.barchart'
view_id = 'cytoflow.view.barchart'
name = "Bar Chart"
short_name = "Bar"
[docs]
def get_view(self):
return BarChartWorkflowView()
[docs]
def get_handler(self, model, context):
if isinstance(model, BarChartWorkflowView):
return BarChartHandler(model = model, context = context)
elif isinstance(model, BarChartPlotParams):
return BarChartParamsHandler(model = model, context = context)
[docs]
def get_icon(self):
return ImageResource('bar_chart')
plugin = List(contributes_to = VIEW_PLUGIN_EXT)
def _plugin_default(self):
return [self]