Plotting#
CORNETO supports plotting of graphs through different backends, such as Graphviz, Pydot, and NetworkX
import corneto as cn
cn.info()
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Using graphviz#
If graphviz and dot are installed, e.g. via conda install python-graphviz, you can use the plot method to visualize the graphs
from corneto.graph import Graph
G = Graph()
G.add_edge(1, 2)
G.add_edge(2, 3)
G.add_edge(1, 3)
G.plot()
# This returns a graphviz object
digraph = G.to_graphviz()
type(digraph)
graphviz.graphs.Digraph
str(digraph)
'digraph {\n\tnode [fixedsize=true]\n\t1 [shape=circle]\n\t2 [shape=circle]\n\t1 -> 2 [arrowhead=normal]\n\t2 [shape=circle]\n\t3 [shape=circle]\n\t2 -> 3 [arrowhead=normal]\n\t1 [shape=circle]\n\t3 [shape=circle]\n\t1 -> 3 [arrowhead=normal]\n}\n'
G.plot_values(edge_values=[-1, 1, 1])
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:76, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
75 kwargs['stdout'] = kwargs['stderr'] = subprocess.PIPE
---> 76 proc = _run_input_lines(cmd, input_lines, kwargs=kwargs)
77 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:96, in _run_input_lines(cmd, input_lines, kwargs)
95 def _run_input_lines(cmd, input_lines, *, kwargs):
---> 96 popen = subprocess.Popen(cmd, stdin=subprocess.PIPE, **kwargs)
98 stdin_write = popen.stdin.write
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1039, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group)
1036 self.stderr = io.TextIOWrapper(self.stderr,
1037 encoding=encoding, errors=errors)
-> 1039 self._execute_child(args, executable, preexec_fn, close_fds,
1040 pass_fds, cwd, env,
1041 startupinfo, creationflags, shell,
1042 p2cread, p2cwrite,
1043 c2pread, c2pwrite,
1044 errread, errwrite,
1045 restore_signals,
1046 gid, gids, uid, umask,
1047 start_new_session, process_group)
1048 except:
1049 # Cleanup if the child failed starting.
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1991, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session, process_group)
1990 if err_filename is not None:
-> 1991 raise child_exception_type(errno_num, err_msg, err_filename)
1992 else:
FileNotFoundError: [Errno 2] No such file or directory: PosixPath('dot')
The above exception was the direct cause of the following exception:
ExecutableNotFound Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/IPython/core/formatters.py:1036, in MimeBundleFormatter.__call__(self, obj, include, exclude)
1033 method = get_real_method(obj, self.print_method)
1035 if method is not None:
-> 1036 return method(include=include, exclude=exclude)
1037 return None
1038 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:98, in JupyterIntegration._repr_mimebundle_(self, include, exclude, **_)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:112, in JupyterIntegration._repr_image_svg_xml(self)
110 def _repr_image_svg_xml(self) -> str:
111 """Return the rendered graph as SVG string."""
--> 112 return self.pipe(format='svg', encoding=SVG_ENCODING)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:104, in Pipe.pipe(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
55 def pipe(self,
56 format: typing.Optional[str] = None,
57 renderer: typing.Optional[str] = None,
(...)
61 engine: typing.Optional[str] = None,
62 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
63 """Return the source piped through the Graphviz layout command.
64
65 Args:
(...)
102 '<?xml version='
103 """
--> 104 return self._pipe_legacy(format,
105 renderer=renderer,
106 formatter=formatter,
107 neato_no_op=neato_no_op,
108 quiet=quiet,
109 engine=engine,
110 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/_tools.py:171, in deprecate_positional_args.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
162 wanted = ', '.join(f'{name}={value!r}'
163 for name, value in deprecated.items())
164 warnings.warn(f'The signature of {func.__name__} will be reduced'
165 f' to {supported_number} positional args'
166 f' {list(supported)}: pass {wanted}'
167 ' as keyword arg(s)',
168 stacklevel=stacklevel,
169 category=category)
--> 171 return func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:121, in Pipe._pipe_legacy(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
112 @_tools.deprecate_positional_args(supported_number=2)
113 def _pipe_legacy(self,
114 format: typing.Optional[str] = None,
(...)
119 engine: typing.Optional[str] = None,
120 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
--> 121 return self._pipe_future(format,
122 renderer=renderer,
123 formatter=formatter,
124 neato_no_op=neato_no_op,
125 quiet=quiet,
126 engine=engine,
127 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:149, in Pipe._pipe_future(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
146 if encoding is not None:
147 if codecs.lookup(encoding) is codecs.lookup(self.encoding):
148 # common case: both stdin and stdout need the same encoding
--> 149 return self._pipe_lines_string(*args, encoding=encoding, **kwargs)
150 try:
151 raw = self._pipe_lines(*args, input_encoding=self.encoding, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/piping.py:212, in pipe_lines_string(engine, format, input_lines, encoding, renderer, formatter, neato_no_op, quiet)
206 cmd = dot_command.command(engine, format,
207 renderer=renderer,
208 formatter=formatter,
209 neato_no_op=neato_no_op)
210 kwargs = {'input_lines': input_lines, 'encoding': encoding}
--> 212 proc = execute.run_check(cmd, capture_output=True, quiet=quiet, **kwargs)
213 return proc.stdout
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:81, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
79 except OSError as e:
80 if e.errno == errno.ENOENT:
---> 81 raise ExecutableNotFound(cmd) from e
82 raise
84 if not quiet and proc.stderr:
ExecutableNotFound: failed to execute PosixPath('dot'), make sure the Graphviz executables are on your systems' PATH
<graphviz.graphs.Digraph at 0x13500e0d0>
G.plot_values(edge_values=[-1, 1, 1], edge_indexes=[0, 1])
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:76, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
75 kwargs['stdout'] = kwargs['stderr'] = subprocess.PIPE
---> 76 proc = _run_input_lines(cmd, input_lines, kwargs=kwargs)
77 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:96, in _run_input_lines(cmd, input_lines, kwargs)
95 def _run_input_lines(cmd, input_lines, *, kwargs):
---> 96 popen = subprocess.Popen(cmd, stdin=subprocess.PIPE, **kwargs)
98 stdin_write = popen.stdin.write
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1039, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group)
1036 self.stderr = io.TextIOWrapper(self.stderr,
1037 encoding=encoding, errors=errors)
-> 1039 self._execute_child(args, executable, preexec_fn, close_fds,
1040 pass_fds, cwd, env,
1041 startupinfo, creationflags, shell,
1042 p2cread, p2cwrite,
1043 c2pread, c2pwrite,
1044 errread, errwrite,
1045 restore_signals,
1046 gid, gids, uid, umask,
1047 start_new_session, process_group)
1048 except:
1049 # Cleanup if the child failed starting.
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1991, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session, process_group)
1990 if err_filename is not None:
-> 1991 raise child_exception_type(errno_num, err_msg, err_filename)
1992 else:
FileNotFoundError: [Errno 2] No such file or directory: PosixPath('dot')
The above exception was the direct cause of the following exception:
ExecutableNotFound Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/IPython/core/formatters.py:1036, in MimeBundleFormatter.__call__(self, obj, include, exclude)
1033 method = get_real_method(obj, self.print_method)
1035 if method is not None:
-> 1036 return method(include=include, exclude=exclude)
1037 return None
1038 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:98, in JupyterIntegration._repr_mimebundle_(self, include, exclude, **_)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:112, in JupyterIntegration._repr_image_svg_xml(self)
110 def _repr_image_svg_xml(self) -> str:
111 """Return the rendered graph as SVG string."""
--> 112 return self.pipe(format='svg', encoding=SVG_ENCODING)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:104, in Pipe.pipe(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
55 def pipe(self,
56 format: typing.Optional[str] = None,
57 renderer: typing.Optional[str] = None,
(...)
61 engine: typing.Optional[str] = None,
62 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
63 """Return the source piped through the Graphviz layout command.
64
65 Args:
(...)
102 '<?xml version='
103 """
--> 104 return self._pipe_legacy(format,
105 renderer=renderer,
106 formatter=formatter,
107 neato_no_op=neato_no_op,
108 quiet=quiet,
109 engine=engine,
110 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/_tools.py:171, in deprecate_positional_args.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
162 wanted = ', '.join(f'{name}={value!r}'
163 for name, value in deprecated.items())
164 warnings.warn(f'The signature of {func.__name__} will be reduced'
165 f' to {supported_number} positional args'
166 f' {list(supported)}: pass {wanted}'
167 ' as keyword arg(s)',
168 stacklevel=stacklevel,
169 category=category)
--> 171 return func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:121, in Pipe._pipe_legacy(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
112 @_tools.deprecate_positional_args(supported_number=2)
113 def _pipe_legacy(self,
114 format: typing.Optional[str] = None,
(...)
119 engine: typing.Optional[str] = None,
120 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
--> 121 return self._pipe_future(format,
122 renderer=renderer,
123 formatter=formatter,
124 neato_no_op=neato_no_op,
125 quiet=quiet,
126 engine=engine,
127 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:149, in Pipe._pipe_future(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
146 if encoding is not None:
147 if codecs.lookup(encoding) is codecs.lookup(self.encoding):
148 # common case: both stdin and stdout need the same encoding
--> 149 return self._pipe_lines_string(*args, encoding=encoding, **kwargs)
150 try:
151 raw = self._pipe_lines(*args, input_encoding=self.encoding, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/piping.py:212, in pipe_lines_string(engine, format, input_lines, encoding, renderer, formatter, neato_no_op, quiet)
206 cmd = dot_command.command(engine, format,
207 renderer=renderer,
208 formatter=formatter,
209 neato_no_op=neato_no_op)
210 kwargs = {'input_lines': input_lines, 'encoding': encoding}
--> 212 proc = execute.run_check(cmd, capture_output=True, quiet=quiet, **kwargs)
213 return proc.stdout
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:81, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
79 except OSError as e:
80 if e.errno == errno.ENOENT:
---> 81 raise ExecutableNotFound(cmd) from e
82 raise
84 if not quiet and proc.stderr:
ExecutableNotFound: failed to execute PosixPath('dot'), make sure the Graphviz executables are on your systems' PATH
<graphviz.graphs.Digraph at 0x1355c0a50>
Using Pydot#
from IPython.display import SVG, display
G_pydot = G.to_dot(backend="pydot")
display(SVG(G_pydot.create_svg()))
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/pydot/core.py:1851, in Dot.create(self, prog, format, encoding)
1850 try:
-> 1851 stdout_data, stderr_data, process = call_graphviz(
1852 program=prog,
1853 arguments=arguments,
1854 working_dir=tmp_dir,
1855 )
1856 except OSError as e:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/pydot/core.py:211, in call_graphviz(program, arguments, working_dir, **kwargs)
209 program_with_args = [program] + arguments
--> 211 process = subprocess.Popen(
212 program_with_args,
213 env=env,
214 cwd=working_dir,
215 shell=False,
216 stderr=subprocess.PIPE,
217 stdout=subprocess.PIPE,
218 **kwargs,
219 )
220 stdout_data, stderr_data = process.communicate()
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1039, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group)
1036 self.stderr = io.TextIOWrapper(self.stderr,
1037 encoding=encoding, errors=errors)
-> 1039 self._execute_child(args, executable, preexec_fn, close_fds,
1040 pass_fds, cwd, env,
1041 startupinfo, creationflags, shell,
1042 p2cread, p2cwrite,
1043 c2pread, c2pwrite,
1044 errread, errwrite,
1045 restore_signals,
1046 gid, gids, uid, umask,
1047 start_new_session, process_group)
1048 except:
1049 # Cleanup if the child failed starting.
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1991, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session, process_group)
1990 if err_filename is not None:
-> 1991 raise child_exception_type(errno_num, err_msg, err_filename)
1992 else:
FileNotFoundError: [Errno 2] No such file or directory: 'dot'
During handling of the above exception, another exception occurred:
FileNotFoundError Traceback (most recent call last)
Cell In[7], line 4
1 from IPython.display import SVG, display
3 G_pydot = G.to_dot(backend="pydot")
----> 4 display(SVG(G_pydot.create_svg()))
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/pydot/core.py:158, in __generate_format_methods.<locals>.__create_method(self, f, prog, encoding)
156 def __create_method(self, f=frmt, prog=None, encoding=None):
157 """Refer to docstring of method `create`."""
--> 158 return self.create(format=f, prog=prog, encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/pydot/core.py:1860, in Dot.create(self, prog, format, encoding)
1858 args = list(e.args)
1859 args[1] = f'"{prog}" not found in path.'
-> 1860 raise OSError(*args)
1861 else:
1862 raise
FileNotFoundError: [Errno 2] "dot" not found in path.
Using NetworkX with Pydot#
import matplotlib.pyplot as plt
import networkx as nx
from networkx.drawing.nx_pydot import from_pydot, graphviz_layout
# Convert pydot to networkx
G_nx = from_pydot(G.to_dot(backend="pydot"))
# Use Graphviz layout (e.g. 'dot' for hierarchies, 'neato' for general layout)
pos = graphviz_layout(G_nx, prog="neato") # 'neato', 'dot', 'fdp', etc.
# Plot with styling
plt.figure(figsize=(3, 3))
nx.draw(
G_nx,
pos,
with_labels=True,
arrows=True,
node_color="lightblue",
edge_color="gray",
node_size=500,
font_size=14,
)
plt.show()
