# GillesPy2 is a modeling toolkit for biochemical simulation.
# Copyright (C) 2019-2024 GillesPy2 developers.
# 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 3 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/>.
import os
import csv
from datetime import datetime
from collections import UserDict, UserList
import numpy as np
from gillespy2.core.jsonify import Jsonify
from gillespy2.core.gillespyError import ValidationError
[docs]def common_rgb_values():
'''
List of 50 hex color values used for plotting graphs
'''
return [
'#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd', '#8c564b', '#e377c2', '#7f7f7f',
'#bcbd22', '#17becf', '#ff0000', '#00ff00', '#0000ff', '#ffff00', '#00ffff', '#ff00ff',
'#800000', '#808000', '#008000', '#800080', '#008080', '#000080', '#ff9999', '#ffcc99',
'#ccff99', '#cc99ff', '#ffccff', '#62666a', '#8896bb', '#77a096', '#9d5a6c', '#9d5a6c',
'#eabc75', '#ff9600', '#885300', '#9172ad', '#a1b9c4', '#18749b', '#dadecf', '#c5b8a8',
'#000117', '#13a8fe', '#cf0060', '#04354b', '#0297a0', '#037665', '#eed284', '#442244',
'#ffddee', '#702afb'
]
def _plot_iterate(self, show_labels=True, included_species_list=[]):
import matplotlib.pyplot as plt # pylint: disable=import-outside-toplevel
for i, species in enumerate(self.data):
if species != 'time':
if species not in included_species_list and included_species_list:
continue
line_color = common_rgb_values()[(i - 1) % len(common_rgb_values())]
if show_labels:
label = species
else:
label = ""
plt.plot(self.data['time'], self.data[species], label=label, color=line_color)
def _plotplotly_iterate(trajectory, show_labels=True, trace_list=None, line_dict=None, included_species_list=[]):
"""
Helper method for Results .plotplotly() method
"""
if trace_list is None:
trace_list = []
import plotly.graph_objs as go # pylint: disable=import-outside-toplevel
for i, species in enumerate(trajectory.data):
if species != 'time':
if species not in included_species_list and included_species_list:
continue
if line_dict is None:
line_dict = {}
# If number of species exceeds number of available colors, loop back through colors
line_dict['color'] = common_rgb_values()[(i-1)%len(common_rgb_values())]
if show_labels:
trace_list.append(
go.Scatter(
x=trajectory.data['time'],
y=trajectory.data[species],
mode='lines',
name=species,
line=line_dict,
legendgroup=species
)
)
else:
trace_list.append(
go.Scatter(
x=trajectory.data['time'],
y=trajectory.data[species],
mode='lines',
name=species,
line=line_dict,
legendgroup=species,
showlegend=False
)
)
return trace_list
[docs]class Trajectory(UserDict, Jsonify):
""" Trajectory Dict created by a gillespy2 solver containing single trajectory, extends the UserDict object.
:param data: A dictionary of trajectory values created by a solver
:type data: UserDict
:param model: The name of the model used to create the trajectory
:type model: str
:param solver_name: The name of the solver used to create the trajectory
:type solver_name: str
:param rc: The solvers status return code.
:type rc: int
:param status: The solver status ('Success','Timed out')
"""
def __init__(self, data, model=None, solver_name="Undefined solver name", rc=0):
self.data = data
self.model = model
self.solver_name = solver_name
self.rc = rc
status_list = {0: 'Success', 33: 'Timed Out'}
self.status = status_list[rc]
def __getitem__(self, key):
if isinstance(key, int):
from gillespy2.core import log # pylint: disable=import-outside-toplevel
species = list(self.data.keys())[key]
msg = "Trajectory is of type dictionary."
msg += f"Use trajectory['[{species}]'] instead of trajectory[{key}]['{species}']"
msg += f"Retrieving trajectory['[{species}]']"
log.warning(msg)
return self.data[species]
if key in self.data:
return self.data[key]
if hasattr(self.__class__, "__missing__"):
return self.__class__.__missing__(self, key)
raise KeyError(key)
[docs]class Results(UserList, Jsonify):
"""
List of Trajectory objects created by a gillespy2 solver, extends the UserList object.
:param data: A list of trajectory objects
:type data: UserList
"""
def __init__(self, data):
self.data = data
def __getattribute__(self, key):
if key in ('model', 'solver_name', 'rc', 'status'):
if len(self.data) > 1:
from gillespy2.core import log # pylint: disable=import-outside-toplevel
msg = f"Results is of type list. Use results[i]['{key}'] instead of results['{key}']"
log.warning(msg)
return getattr(Results.__getattribute__(self, key='data')[0], key)
return UserList.__getattribute__(self, key)
def __getitem__(self, key):
if key == 'data':
return UserList.__getitem__(self, key)
if isinstance(key, str):
if len(self.data) > 1:
from gillespy2.core import log # pylint: disable=import-outside-toplevel
msg = f"Results is of type list. Use results[i]['{key}'] instead of results['{key}']"
log.warning(msg)
return self.data[0][key]
return UserList.__getitem__(self,key)
def __add__(self, other):
combined_data = Results(data=(self.data + other.data))
consistent_solver = combined_data._validate_solver()
consistent_model = combined_data._validate_model()
if not consistent_solver:
from gillespy2.core import log # pylint: disable=import-outside-toplevel
log.warning("Results objects contain Trajectory objects from multiple solvers.")
if not consistent_model:
raise ValidationError('Results objects contain Trajectory objects from multiple models.')
return combined_data
def __radd__(self, other):
if other == 0:
return self
return self.__add__(other)
def _validate_model(self, reference=None):
is_valid = True
if reference is not None:
reference_model = reference
else:
reference_model = self.data[0].model.get_json_hash()
for trajectory in self.data:
if trajectory.model.get_json_hash() != reference_model:
is_valid = False
return is_valid
def _validate_solver(self, reference=None):
is_valid = True
if reference is not None:
reference_solver = reference
else:
reference_solver = self.data[0].solver_name
for trajectory in self.data:
if trajectory.solver_name != reference_solver:
is_valid = False
return is_valid
def _validate_title(self, show_title):
if not show_title:
title = ''
return title
if self._validate_model():
title_model = self.data[0].model.name
else:
title_model = 'Multiple Models'
if self._validate_solver():
title_solver = self.data[0].solver_name
else:
title_solver = 'Multiple Solvers'
title = (title_model + " - " + title_solver)
return title
[docs] def to_array(self):
'''
Convert the results object into a numpy array.
:returns: Array containing the result of the simulation.
:rtype: numpy.ndarray
'''
results = []
size1 = len(self.data[0]['time'])
size2 = len(self.data[0])
for trajectory in self.data:
new_array = np.zeros((size1, size2))
for j, key in enumerate(trajectory):
new_array[:, j] = trajectory[key]
results.append(new_array)
return np.array(results)
[docs] @classmethod
def build_from_solver_results(cls, solver, live_output_options):
"""
Build a gillespy2.Results object using the provided solver results.
:param solver: The solver used to run the simulation.
:type solver: gillespy2.GillesPySolver
:param live_output_options: dictionary contains options for live_output. By default {"interval":1}.
"interval" specifies seconds between displaying.
"clear_output" specifies if display should be refreshed with each display
:type live_output_options: dict
"""
if solver.rc == 33:
from gillespy2.core import log # pylint: disable=import-outside-toplevel
log.warning('GillesPy2 simulation exceeded timeout.')
if hasattr(solver.result[0], 'shape'):
return solver.result
if len(solver.result) > 0:
results_list = []
for result in solver.result:
temp = Trajectory(data=result, model=solver.model, solver_name=solver.name, rc=solver.rc)
results_list.append(temp)
results = Results(results_list)
if "type" in live_output_options.keys() and live_output_options['type'] == "graph":
results.plot()
return results
raise ValueError("number_of_trajectories must be non-negative and non-zero")
[docs] def to_csv(self, path=".", nametag=None, stamp=None, suffix=".odf", verbose=False):
"""
Outputs the Results to one or more .csv files in a new directory.
:param nametag: allows the user to optionally "tag" the directory and included files. Defaults to the model
name.
:type nametag: str
:param path: the location for the new directory and included files. Defaults to model location.
:type path: str
:param stamp: Allows the user to optionally "tag" the directory (not included files). Default is timestamp.
:type stamp: str
:param verbose: Print useful informataion.
:type verbose: str
:returns: Path to the observed data files.
:rtype: str
"""
if stamp is None:
now = datetime.now()
stamp = datetime.timestamp(now)
if nametag is None:
identifier = self._validate_title(show_title=True)
else:
identifier = nametag
directory = os.path.join(path, f"{identifier}-{stamp}{suffix}")
if verbose:
print(f"Writing data to: {directory}")
# multiple trajectories
if isinstance(self.data, list):
os.makedirs(directory)
for i, trajectory in enumerate(self.data): # write each CSV file
filename = os.path.join(directory, str(identifier)+str(i)+".csv")
field_names = []
for species in trajectory: # build the header
field_names.append(species)
with open(filename, 'w', newline='', encoding="utf-8") as csv_file:
csv_writer = csv.writer(csv_file)
csv_writer.writerow(field_names) # write the header
for j, _ in enumerate(trajectory['time']): # write all lines of the CSV file
this_line=[]
for species in trajectory: # build one line of the CSV file
this_line.append(trajectory[species][j])
csv_writer.writerow(this_line) # write one line of the CSV file
return directory
[docs] def plot(self, index=None, xaxis_label="Time", xscale='linear', yscale='linear', yaxis_label="Value",
style="default", title=None, show_title=False, show_legend=True, multiple_graphs=False,
included_species_list=[], save_png=False, figsize=(18, 10)):
"""
Plots the Results using matplotlib.
:param index: If not none, the index of the Trajectory to be plotted.
:type index: int
:param xaxis_label: The label for the x-axis
:type xaxis_label: str
:param yaxis_label: The label for the y-axis
:type yaxis_label: str
:param title: The title of the graph
:type title: str
:param multiple_graphs: IF each trajectory should have its own graph or if they should overlap.
:type multiple_graphs: bool
:param included_species_list: A list of strings describing which species to include. By default displays all
species.
:type included_species_list: list
:param save_png: Should the graph be saved as a png file. If True, File name is title of graph. If a string is
given, file is named after that string.
:type save_png: bool or str
:param figsize: The size of the graph. A tuple of the form (width,height). Is (18,10) by default.
:type figsize: tuple of ints (x,y)
"""
import matplotlib.pyplot as plt # pylint: disable=import-outside-toplevel
from collections.abc import Iterable # pylint: disable=import-outside-toplevel
trajectory_list = []
if isinstance(index, Iterable):
for i in index:
trajectory_list.append(self.data[i])
elif isinstance(index, int):
trajectory_list.append(self.data[index])
else:
trajectory_list = self.data
if title is None:
title = self._validate_title(show_title)
if len(trajectory_list) < 2:
multiple_graphs = False
if multiple_graphs:
for i, trajectory in enumerate(trajectory_list):
result = Results(data=[trajectory])
if isinstance(save_png, str):
result.plot(xaxis_label=xaxis_label, yaxis_label=yaxis_label, title=title + " " + str(i + 1),
style=style, included_species_list=included_species_list, save_png=save_png + str(i + 1)
, figsize=figsize)
else:
result.plot(xaxis_label=xaxis_label, yaxis_label=yaxis_label, title=title + " " + str(i + 1),
style=style, included_species_list=included_species_list, save_png=save_png,
figsize=figsize)
else:
try:
plt.style.use(style)
except Exception:
from gillespy2.core import log # pylint: disable=import-outside-toplevel
msg = f"Invalid matplotlib style. Try using one of the following {plt.style.available}"
log.warning(msg)
plt.style.use("default")
plt.figure(figsize=figsize)
plt.title(title, fontsize=18)
plt.xlabel(xaxis_label)
plt.ylabel(yaxis_label)
plt.xscale(xscale)
plt.yscale(yscale)
for i, trajectory in enumerate(trajectory_list):
if i > 0:
_plot_iterate(trajectory, included_species_list=included_species_list, show_labels=False)
else:
_plot_iterate(trajectory, included_species_list=included_species_list)
if show_legend:
plt.legend(loc='best')
plt.plot()
if isinstance(save_png, str):
plt.savefig(save_png)
elif save_png:
plt.savefig(title)
[docs] def plotplotly(self, index=None, xaxis_label="Time", yaxis_label="Value", title=None,
show_title=False, show_legend=True, multiple_graphs=False, included_species_list=[],
return_plotly_figure=False, **layout_args):
""" Plots the Results using plotly. Can only be viewed in a Jupyter Notebook.
:param index: If not none, the index of the Trajectory to be plotted.
:type index: int
:param xaxis_label: The label for the x-axis
:type xaxis_label: str
:param yaxis_label: The label for the y-axis
:type yaxis_label: str
:param title: The title of the graph
:type title: str
:param show_title: If True, title will be shown on graph.
:type show_title: bool
:param show_legend: Default True, if False, legend will not be shown on graph.
:type show_legend: bool
:param multiple_graphs: IF each trajectory should have its own graph or if they should overlap.
:type multiple_graphs: bool
:param included_species_list: A list of strings describing which species to include. By default displays all
species.
:type included_species_list: list
:param return_plotly_figure: Whether or not to return a figure dictionary of data(graph object traces) and
layout which may be edited by the user
:type return_plotly_figure: bool
:param **layout_args: Optional additional arguments to be passed to plotlys layout constructor.
:type **layout_args: dict
"""
from plotly.offline import init_notebook_mode, iplot # pylint: disable=import-outside-toplevel
import plotly.graph_objs as go # pylint: disable=import-outside-toplevel
# Backwards compatibility with xaxis_label argument (which duplicates plotly's xaxis_title argument)
if layout_args.get('xaxis_title') is not None:
xaxis_label = layout_args.get('xaxis_title')
layout_args.pop('xaxis_title')
if layout_args.get('yaxis_title') is not None:
yaxis_label = layout_args.get('yaxis_title')
layout_args.pop('yaxis_title')
init_notebook_mode()
from collections.abc import Iterable # pylint: disable=import-outside-toplevel
trajectory_list = []
if isinstance(index, Iterable):
for i in index:
trajectory_list.append(self.data[i])
elif isinstance(index, int):
trajectory_list.append(self.data[index])
else:
trajectory_list = self.data
number_of_trajectories = len(trajectory_list)
if title is None:
title = self._validate_title(show_title)
fig = dict(data=[], layout=[])
if len(trajectory_list) < 2:
multiple_graphs = False
if multiple_graphs:
from plotly import subplots # pylint: disable=import-outside-toplevel
fig = subplots.make_subplots(print_grid=False, rows=int(number_of_trajectories/2) +
int(number_of_trajectories % 2), cols=2)
for i, trajectory in enumerate(trajectory_list):
if i > 0:
trace_list = _plotplotly_iterate(trajectory, trace_list=[], included_species_list=
included_species_list, show_labels=False)
else:
trace_list = _plotplotly_iterate(trajectory, trace_list=[], included_species_list=
included_species_list)
for trace in trace_list:
if i % 2 == 0:
fig.append_trace(trace, int(i/2) + 1, 1)
else:
fig.append_trace(trace, int(i/2) + 1, 2)
fig['layout'].update(
autosize=True, height=400*len(trajectory_list), showlegend=show_legend, title=title
)
else:
trace_list = []
for i, trajectory in enumerate(trajectory_list):
if i > 0:
trace_list = _plotplotly_iterate(trajectory, trace_list=trace_list, included_species_list=
included_species_list, show_labels=False)
else:
trace_list = _plotplotly_iterate(trajectory, trace_list=trace_list, included_species_list=
included_species_list)
layout = go.Layout(
showlegend=show_legend,
title=title,
xaxis_title=xaxis_label,
yaxis_title=yaxis_label,
**layout_args
)
fig['data'] = trace_list
fig['layout'] = layout
if not return_plotly_figure:
iplot(fig)
return None
return fig
[docs] def average_ensemble(self):
"""
Generate a single Results object with a Trajectory that is made of the means of all trajectories' outputs
:returns: The Results object
"""
trajectory_list = self.data
number_of_trajectories = len(trajectory_list)
output_trajectory = Trajectory(data={}, model=trajectory_list[0].model, solver_name=
trajectory_list[0].solver_name)
for species in trajectory_list[0]: # Initialize the output to be the same size as the inputs
output_trajectory[species] = [0]*len(trajectory_list[0][species])
output_trajectory['time'] = trajectory_list[0]['time']
# Add every value of every Trajectory Dict into one output Trajectory
for i in range(0, number_of_trajectories):
trajectory_dict = trajectory_list[i]
for species in trajectory_dict:
if species == 'time':
continue
for k in range(0, len(output_trajectory[species])):
output_trajectory[species][k] += trajectory_dict[species][k]
for species in output_trajectory: # Divide for mean of every value in output Trajectory
if species == 'time':
continue
for i in range(0, len(output_trajectory[species])):
output_trajectory[species][i] /= number_of_trajectories
output_results = Results(data=[output_trajectory]) # package output_trajectory in a Results object
return output_results
[docs] def stddev_ensemble(self, ddof=0):
"""
Generate a single Results object with a Trajectory that is made of the sample standard deviations of all
trajectories' outputs.
:param ddof: Delta Degrees of Freedom. The divisor used in calculations is N - ddof, where N represents
the number of trajectories. Sample standard deviation uses ddof of 1. Defaults to population standard
deviation where ddof is 0.
:type ddof: int
:returns: the Results object
"""
from math import sqrt # pylint: disable=import-outside-toplevel
trajectory_list = self.data
number_of_trajectories = len(trajectory_list)
if ddof == number_of_trajectories:
from gillespy2.core import log # pylint: disable=import-outside-toplevel
log.warning("ddof must be less than the number of trajectories. Using ddof of 0")
ddof = 0
average_list = self.average_ensemble().data[0]
output_trajectory = Trajectory(data={}, model=trajectory_list[0].model, solver_name=
trajectory_list[0].solver_name)
for species in trajectory_list[0]: # Initialize the output to be the same size as the inputs
output_trajectory[species] = [0]*len(trajectory_list[0][species])
output_trajectory['time'] = trajectory_list[0]['time']
for i in range(0, number_of_trajectories):
trajectory_dict = trajectory_list[i]
for species in trajectory_dict:
if species == 'time':
continue
for k in range(0, len(output_trajectory['time'])):
output_trajectory[species][k] += (trajectory_dict[species][k] - average_list[species][k])\
* (trajectory_dict[species][k] - average_list[species][k])
for species in output_trajectory: # Divide for mean of every value in output Trajectory
if species == 'time':
continue
for i in range(0, len(output_trajectory[species])):
output_trajectory[species][i] /= (number_of_trajectories - ddof)
output_trajectory[species][i] = sqrt(output_trajectory[species][i])
output_results = Results(data=[output_trajectory]) # package output_trajectory in a Results object
return output_results
[docs] def plotplotly_mean_stdev(self, xaxis_label="Time", yaxis_label="Value", title=None,
show_title=False, show_legend=True, included_species_list=[],
return_plotly_figure=False, ddof=0, **layout_args):
"""
Plot a plotly graph depicting the mean and standard deviation of a results object
:param xaxis_label: The label for the x-axis
:type xaxis_label: str
:param yaxis_label: The label for the y-axis
:type yaxis_label: str
:param title: The title of the graph
:type title: str
:param show_title: If True, title will be shown on graph.
:type show_title: bool
:param show_legend: Default True, if False, legend will not be shown on graph.
:type show_legend: bool
:param included_species_list: A list of strings describing which species to include. By default displays all
species.
:type included_species_list: list
:param return_plotly_figure: Whether or not to return a figure dicctionary of data(graph object traces) and
layout which may be edited by the user
:type return_plotly_figure: bool
:param ddof: Delta Degrees of Freedom. The divisor used in calculations is N - ddof, where N represents
the number of trajectories. Sample standard deviation uses ddof of 1. Defaults to population standard
deviation where ddof is 0.
:type ddof: int
:param **layout_args: Optional additional arguments to be passed to plotlys layout constructor.
:type **layout_args: dict
"""
# Backwards compatibility with xaxis_label argument (which duplicates plotly's xaxis_title argument)
if layout_args.get('xaxis_title') is not None:
xaxis_label = layout_args.get('xaxis_title')
layout_args.pop('xaxis_title')
if layout_args.get('yaxis_title') is not None:
yaxis_label = layout_args.get('yaxis_title')
layout_args.pop('yaxis_title')
average_trajectory = self.average_ensemble().data[0]
stddev_trajectory = self.stddev_ensemble(ddof=ddof).data[0]
from plotly.offline import init_notebook_mode, iplot # pylint: disable=import-outside-toplevel
import plotly.graph_objs as go # pylint: disable=import-outside-toplevel
init_notebook_mode()
if not show_title:
title = 'Mean and Standard Deviation'
else:
if title is None:
title = (self._validate_title(show_title) + " - Mean and Standard Deviation")
trace_list = []
for species in average_trajectory:
if species != 'time':
if species not in included_species_list and included_species_list:
continue
upper_bound = []
lower_bound = []
for i in range(0, len(average_trajectory[species])):
upper_bound.append(average_trajectory[species][i] + stddev_trajectory[species][i])
lower_bound.append(average_trajectory[species][i] - stddev_trajectory[species][i])
# Append upper_bound list to trace_list
trace_list.append(
go.Scatter(
name=species + ' Upper Bound',
x=average_trajectory['time'],
y=upper_bound,
mode='lines',
marker=dict(color="#444"),
line=dict(width=1, dash='dot'),
legendgroup=str(average_trajectory[species]),
showlegend=False
)
)
trace_list.append(
go.Scatter(
x=average_trajectory['time'],
y=average_trajectory[species],
name=species,
fillcolor='rgba(68, 68, 68, 0.2)',
fill='tonexty',
legendgroup=str(average_trajectory[species]),
)
)
# Append lower_bound list to trace_list
trace_list.append(
go.Scatter(
name=species + ' Lower Bound',
x=average_trajectory['time'],
y= lower_bound,
mode='lines',
marker=dict(color="#444"),
line=dict(width=1, dash='dot'),
fillcolor='rgba(68, 68, 68, 0.2)',
fill='tonexty',
legendgroup=str(average_trajectory[species]),
showlegend=False
)
)
layout = go.Layout(
showlegend=show_legend,
title=title,
xaxis_title=xaxis_label,
yaxis_title=yaxis_label,
legend={'traceorder': 'normal'},
**layout_args
)
fig = dict(data=trace_list, layout=layout)
if not return_plotly_figure:
iplot(fig)
return None
return fig
[docs] def plot_mean_stdev(self, xscale='linear', yscale='linear', xaxis_label="Time", yaxis_label="Value"
, title=None, show_title=False, style="default", show_legend=True, included_species_list=[],
ddof=0, save_png=False, figsize=(18, 10)):
"""
Plot a matplotlib graph depicting mean and standard deviation of a results object.
:param xaxis_label: The label for the x-axis
:type xaxis_label: str
:param yaxis_label: The label for the y-axis
:type yaxis_label: str
:param title: The title of the graph
:type title: str
:param show_title: Default False, if True, title will be displayed on the graph.
:type show_title: bool
:param style: Matplotlib style to be displayed on graph.
:type style: str
:param show_legend: Default to True, if False, legend will not be shown on graph.
:type show_legend: bool
:param included_species_list: A list of strings describing which species to include. By default displays all
species.
:type included_species_list: list
:param ddof: Delta Degrees of Freedom. The divisor used in calculations is N - ddof, where N represents
the number of trajectories. Sample standard deviation uses ddof of 1. Defaults to population standard
deviation where ddof is 0.
:type ddof: int
:type save_png: bool or str
:param figsize: The size of the graph. A tuple of the form (width,height). Is (18,10) by default.
:type figsize: tuple of ints (x,y)
"""
average_result = self.average_ensemble().data[0]
stddev_trajectory = self.stddev_ensemble(ddof=ddof).data[0]
import matplotlib.pyplot as plt # pylint: disable=import-outside-toplevel
try:
plt.style.use(style)
except Exception:
from gillespy2.core import log # pylint: disable=import-outside-toplevel
msg = f"Invalid matplotlib style. Try using one of the following {plt.style.available}"
log.warning(msg)
plt.style.use("default")
plt.figure(figsize=figsize)
for species in average_result:
if species == 'time':
continue
if species not in included_species_list and included_species_list:
continue
lower_bound = [a-b for a, b in zip(average_result[species], stddev_trajectory[species])]
upper_bound = [a+b for a, b in zip(average_result[species], stddev_trajectory[species])]
plt.fill_between(average_result['time'], lower_bound, upper_bound, color='whitesmoke')
plt.plot(average_result['time'], upper_bound, color='grey', linestyle='dashed')
plt.plot(average_result['time'], lower_bound, color='grey', linestyle='dashed')
plt.plot(average_result['time'], average_result[species], label=species)
if not show_title:
title = 'Mean and Standard Deviation'
else:
if title is None:
title = (self._validate_title(show_title) + " - Mean and Standard Deviation")
plt.title(title, fontsize=18)
plt.xlabel(xaxis_label)
plt.ylabel(yaxis_label)
plt.xscale(xscale)
plt.yscale(yscale)
plt.plot([0], [11])
if show_legend:
plt.legend(loc='best')
if isinstance(save_png, str):
plt.savefig(save_png)
elif save_png:
plt.savefig(title)
# for backwards compatability, we need to keep the old name around
[docs] def plotplotly_std_dev_range(self, **kwargs):
"""
Plot a plotly graph depicting the mean and standard deviation of a results object
:param xaxis_label: The label for the x-axis
:type xaxis_label: str
:param yaxis_label: The label for the y-axis
:type yaxis_label: str
:param title: The title of the graph
:type title: str
:param show_title: If True, title will be shown on graph.
:type show_title: bool
:param show_legend: Default True, if False, legend will not be shown on graph.
:type show_legend: bool
:param included_species_list: A list of strings describing which species to include. By default displays all
species.
:type included_species_list: list
:param return_plotly_figure: Whether or not to return a figure dicctionary of data(graph object traces) and
layout which may be edited by the user
:type return_plotly_figure: bool
:param ddof: Delta Degrees of Freedom. The divisor used in calculations is N - ddof, where N represents
the number of trajectories. Sample standard deviation uses ddof of 1. Defaults to population standard
deviation where ddof is 0.
:type ddof: int
:param **layout_args: Optional additional arguments to be passed to plotlys layout constructor.
:type **layout_args: dict
"""
from gillespy2.core import log # pylint: disable=import-outside-toplevel
log.warning(
"The plotplotly_std_dev_range function has been deprecated. This function will be removed in a "
"future release. Please use plotplotly_mean_stdev instead."
)
self.plotplotly_mean_stdev(**kwargs)
# for backwards compatability, we need to keep the old name around
[docs] def plot_std_dev_range(self, **kwargs):
"""
Plot a matplotlib graph depicting mean and standard deviation of a results object.
:param xaxis_label: The label for the x-axis
:type xaxis_label: str
:param yaxis_label: The label for the y-axis
:type yaxis_label: str
:param title: The title of the graph
:type title: str
:param show_title: Default False, if True, title will be displayed on the graph.
:type show_title: bool
:param style: Matplotlib style to be displayed on graph.
:type style: str
:param show_legend: Default to True, if False, legend will not be shown on graph.
:type show_legend: bool
:param included_species_list: A list of strings describing which species to include. By default displays all
species.
:type included_species_list: list
:param ddof: Delta Degrees of Freedom. The divisor used in calculations is N - ddof, where N represents
the number of trajectories. Sample standard deviation uses ddof of 1. Defaults to population standard
deviation where ddof is 0.
:type ddof: int
:type save_png: bool or str
:param figsize: The size of the graph. A tuple of the form (width,height). Is (18,10) by default.
:type figsize: tuple of ints (x,y)
"""
from gillespy2.core import log # pylint: disable=import-outside-toplevel
log.warning(
"The plot_std_dev_range function has been deprecated. This function will be removed in a "
"future release. Please use plot_mean_stdev instead."
)
self.plot_mean_stdev(**kwargs)
