#!/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/>.
"""
1D Statistics Plot
------------------
Plots a line plot 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.
.. object:: Feature
The column in the statistic to plot on the Y axis (often a channel name.)
.. object:: Variable
The statistic variable put on the X axis. Must be numeric.
.. object:: X Scale, Y Scale
How to scale the X and Y axes.
.. 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:: Color Scale
If **Color Facet** is a numeric variable, use this scale for the color
bar.
.. 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()
ch_op = flow.ChannelStatisticOp(name = 'MeanByDox',
channel = 'Y2-A',
function = flow.geom_mean,
by = ['Dox'])
ex2 = ch_op.apply(ex)
flow.Stats1DView(variable = 'Dox',
statistic = 'MeanByDox',
feature = 'Y2-A',
scale = 'log',
variable_scale = 'log').plot(ex2)
"""
import pandas as pd
from traits.api import provides, Property, List
from traitsui.api import View, Item, EnumEditor, VGroup, TextEditor, Controller, TupleEditor
from envisage.api import Plugin
from pyface.api import ImageResource # @UnresolvedImport
import cytoflow.utility as util
from ..workflow.views import Stats1DWorkflowView, Stats1DPlotParams
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 Stats1DParamsHandler(Controller):
view_params_view = \
View(Item('variable_lim',
label = "Variable\nLimits",
editor = TupleEditor(editors = [TextEditor(auto_set = False,
evaluate = float,
format_func = lambda x: "" if x == None else str(x)),
TextEditor(auto_set = False,
evaluate = float,
format_func = lambda x: "" if x == None else str(x))],
labels = ["Min", "Max"],
cols = 1)),
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'),
Item('shade_error'),
Item('shade_alpha'),
Stats1DPlotParamsView.content)
[docs]
class Stats1DHandler(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('feature',
editor = EnumEditor(name='handler.features'),
label = "Feature"),
Item('scale', label = "Statistic\nScale"),
Item('variable',
editor = EnumEditor(name = 'handler.numeric_indices')),
Item('variable_scale', label = "Variable\nScale"),
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('huescale',
label = "Hue\nScale"),
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 = "One-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 = Stats1DParamsHandler),
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 Stats1DPlugin(Plugin, PluginHelpMixin):
id = 'cytoflowgui.view.stats1d'
view_id = 'cytoflow.view.stats1d'
name = "1D Statistics View"
short_name = "Stats 1D"
[docs]
def get_view(self):
return Stats1DWorkflowView()
[docs]
def get_handler(self, model, context):
if isinstance(model, Stats1DWorkflowView):
return Stats1DHandler(model = model, context = context)
elif isinstance(model, Stats1DPlotParams):
return Stats1DParamsHandler(model = model, context = context)
[docs]
def get_icon(self):
return ImageResource('stats_1d')
plugin = List(contributes_to = VIEW_PLUGIN_EXT)
def _plugin_default(self):
return [self]