"""
******
Layout
******
Node positioning algorithms for graph drawing.
For `random_layout()` the possible resulting shape
is a square of side [0, scale] (default: [0, 1])
Changing `center` shifts the layout by that amount.
For the other layout routines, the extent is
[center - scale, center + scale] (default: [-1, 1]).
Warning: Most layout routines have only been tested in 2-dimensions.
"""
import networkx as nx
from networkx.utils import np_random_state
__all__ = [
"bipartite_layout",
"circular_layout",
"forceatlas2_layout",
"kamada_kawai_layout",
"random_layout",
"rescale_layout",
"rescale_layout_dict",
"shell_layout",
"spring_layout",
"spectral_layout",
"planar_layout",
"fruchterman_reingold_layout",
"spiral_layout",
"multipartite_layout",
"bfs_layout",
"arf_layout",
]
def _process_params(G, center, dim):
# Some boilerplate code.
import numpy as np
if not isinstance(G, nx.Graph):
empty_graph = nx.Graph()
empty_graph.add_nodes_from(G)
G = empty_graph
if center is None:
center = np.zeros(dim)
else:
center = np.asarray(center)
if len(center) != dim:
msg = "length of center coordinates must match dimension of layout"
raise ValueError(msg)
return G, center
[docs]
@np_random_state(3)
def random_layout(G, center=None, dim=2, seed=None):
"""Position nodes uniformly at random in the unit square.
For every node, a position is generated by choosing each of dim
coordinates uniformly at random on the interval [0.0, 1.0).
NumPy (http://scipy.org) is required for this function.
Parameters
----------
G : NetworkX graph or list of nodes
A position will be assigned to every node in G.
center : array-like or None
Coordinate pair around which to center the layout.
dim : int
Dimension of layout.
seed : int, RandomState instance or None optional (default=None)
Set the random state for deterministic node layouts.
If int, `seed` is the seed used by the random number generator,
if numpy.random.RandomState instance, `seed` is the random
number generator,
if None, the random number generator is the RandomState instance used
by numpy.random.
Returns
-------
pos : dict
A dictionary of positions keyed by node
Examples
--------
>>> G = nx.lollipop_graph(4, 3)
>>> pos = nx.random_layout(G)
"""
import numpy as np
G, center = _process_params(G, center, dim)
pos = seed.rand(len(G), dim) + center
pos = pos.astype(np.float32)
pos = dict(zip(G, pos))
return pos
[docs]
def circular_layout(G, scale=1, center=None, dim=2):
# dim=2 only
"""Position nodes on a circle.
Parameters
----------
G : NetworkX graph or list of nodes
A position will be assigned to every node in G.
scale : number (default: 1)
Scale factor for positions.
center : array-like or None
Coordinate pair around which to center the layout.
dim : int
Dimension of layout.
If dim>2, the remaining dimensions are set to zero
in the returned positions.
If dim<2, a ValueError is raised.
Returns
-------
pos : dict
A dictionary of positions keyed by node
Raises
------
ValueError
If dim < 2
Examples
--------
>>> G = nx.path_graph(4)
>>> pos = nx.circular_layout(G)
Notes
-----
This algorithm currently only works in two dimensions and does not
try to minimize edge crossings.
"""
import numpy as np
if dim < 2:
raise ValueError("cannot handle dimensions < 2")
G, center = _process_params(G, center, dim)
paddims = max(0, (dim - 2))
if len(G) == 0:
pos = {}
elif len(G) == 1:
pos = {nx.utils.arbitrary_element(G): center}
else:
# Discard the extra angle since it matches 0 radians.
theta = np.linspace(0, 1, len(G) + 1)[:-1] * 2 * np.pi
theta = theta.astype(np.float32)
pos = np.column_stack(
[np.cos(theta), np.sin(theta), np.zeros((len(G), paddims))]
)
pos = rescale_layout(pos, scale=scale) + center
pos = dict(zip(G, pos))
return pos
[docs]
def shell_layout(G, nlist=None, rotate=None, scale=1, center=None, dim=2):
"""Position nodes in concentric circles.
Parameters
----------
G : NetworkX graph or list of nodes
A position will be assigned to every node in G.
nlist : list of lists
List of node lists for each shell.
rotate : angle in radians (default=pi/len(nlist))
Angle by which to rotate the starting position of each shell
relative to the starting position of the previous shell.
To recreate behavior before v2.5 use rotate=0.
scale : number (default: 1)
Scale factor for positions.
center : array-like or None
Coordinate pair around which to center the layout.
dim : int
Dimension of layout, currently only dim=2 is supported.
Other dimension values result in a ValueError.
Returns
-------
pos : dict
A dictionary of positions keyed by node
Raises
------
ValueError
If dim != 2
Examples
--------
>>> G = nx.path_graph(4)
>>> shells = [[0], [1, 2, 3]]
>>> pos = nx.shell_layout(G, shells)
Notes
-----
This algorithm currently only works in two dimensions and does not
try to minimize edge crossings.
"""
import numpy as np
if dim != 2:
raise ValueError("can only handle 2 dimensions")
G, center = _process_params(G, center, dim)
if len(G) == 0:
return {}
if len(G) == 1:
return {nx.utils.arbitrary_element(G): center}
if nlist is None:
# draw the whole graph in one shell
nlist = [list(G)]
radius_bump = scale / len(nlist)
if len(nlist[0]) == 1:
# single node at center
radius = 0.0
else:
# else start at r=1
radius = radius_bump
if rotate is None:
rotate = np.pi / len(nlist)
first_theta = rotate
npos = {}
for nodes in nlist:
# Discard the last angle (endpoint=False) since 2*pi matches 0 radians
theta = (
np.linspace(0, 2 * np.pi, len(nodes), endpoint=False, dtype=np.float32)
+ first_theta
)
pos = radius * np.column_stack([np.cos(theta), np.sin(theta)]) + center
npos.update(zip(nodes, pos))
radius += radius_bump
first_theta += rotate
return npos
[docs]
def bipartite_layout(
G, nodes, align="vertical", scale=1, center=None, aspect_ratio=4 / 3
):
"""Position nodes in two straight lines.
Parameters
----------
G : NetworkX graph or list of nodes
A position will be assigned to every node in G.
nodes : list or container
Nodes in one node set of the bipartite graph.
This set will be placed on left or top.
align : string (default='vertical')
The alignment of nodes. Vertical or horizontal.
scale : number (default: 1)
Scale factor for positions.
center : array-like or None
Coordinate pair around which to center the layout.
aspect_ratio : number (default=4/3):
The ratio of the width to the height of the layout.
Returns
-------
pos : dict
A dictionary of positions keyed by node.
Examples
--------
>>> G = nx.bipartite.gnmk_random_graph(3, 5, 10, seed=123)
>>> top = nx.bipartite.sets(G)[0]
>>> pos = nx.bipartite_layout(G, top)
Notes
-----
This algorithm currently only works in two dimensions and does not
try to minimize edge crossings.
"""
import numpy as np
if align not in ("vertical", "horizontal"):
msg = "align must be either vertical or horizontal."
raise ValueError(msg)
G, center = _process_params(G, center=center, dim=2)
if len(G) == 0:
return {}
height = 1
width = aspect_ratio * height
offset = (width / 2, height / 2)
top = dict.fromkeys(nodes)
bottom = [v for v in G if v not in top]
nodes = list(top) + bottom
left_xs = np.repeat(0, len(top))
right_xs = np.repeat(width, len(bottom))
left_ys = np.linspace(0, height, len(top))
right_ys = np.linspace(0, height, len(bottom))
top_pos = np.column_stack([left_xs, left_ys]) - offset
bottom_pos = np.column_stack([right_xs, right_ys]) - offset
pos = np.concatenate([top_pos, bottom_pos])
pos = rescale_layout(pos, scale=scale) + center
if align == "horizontal":
pos = pos[:, ::-1] # swap x and y coords
pos = dict(zip(nodes, pos))
return pos
[docs]
@np_random_state(10)
def spring_layout(
G,
k=None,
pos=None,
fixed=None,
iterations=50,
threshold=1e-4,
weight="weight",
scale=1,
center=None,
dim=2,
seed=None,
):
"""Position nodes using Fruchterman-Reingold force-directed algorithm.
The algorithm simulates a force-directed representation of the network
treating edges as springs holding nodes close, while treating nodes
as repelling objects, sometimes called an anti-gravity force.
Simulation continues until the positions are close to an equilibrium.
There are some hard-coded values: minimal distance between
nodes (0.01) and "temperature" of 0.1 to ensure nodes don't fly away.
During the simulation, `k` helps determine the distance between nodes,
though `scale` and `center` determine the size and place after
rescaling occurs at the end of the simulation.
Fixing some nodes doesn't allow them to move in the simulation.
It also turns off the rescaling feature at the simulation's end.
In addition, setting `scale` to `None` turns off rescaling.
Parameters
----------
G : NetworkX graph or list of nodes
A position will be assigned to every node in G.
k : float (default=None)
Optimal distance between nodes. If None the distance is set to
1/sqrt(n) where n is the number of nodes. Increase this value
to move nodes farther apart.
pos : dict or None optional (default=None)
Initial positions for nodes as a dictionary with node as keys
and values as a coordinate list or tuple. If None, then use
random initial positions.
fixed : list or None optional (default=None)
Nodes to keep fixed at initial position.
Nodes not in ``G.nodes`` are ignored.
ValueError raised if `fixed` specified and `pos` not.
iterations : int optional (default=50)
Maximum number of iterations taken
threshold: float optional (default = 1e-4)
Threshold for relative error in node position changes.
The iteration stops if the error is below this threshold.
weight : string or None optional (default='weight')
The edge attribute that holds the numerical value used for
the edge weight. Larger means a stronger attractive force.
If None, then all edge weights are 1.
scale : number or None (default: 1)
Scale factor for positions. Not used unless `fixed is None`.
If scale is None, no rescaling is performed.
center : array-like or None
Coordinate pair around which to center the layout.
Not used unless `fixed is None`.
dim : int
Dimension of layout.
seed : int, RandomState instance or None optional (default=None)
Used only for the initial positions in the algorithm.
Set the random state for deterministic node layouts.
If int, `seed` is the seed used by the random number generator,
if numpy.random.RandomState instance, `seed` is the random
number generator,
if None, the random number generator is the RandomState instance used
by numpy.random.
Returns
-------
pos : dict
A dictionary of positions keyed by node
Examples
--------
>>> G = nx.path_graph(4)
>>> pos = nx.spring_layout(G)
# The same using longer but equivalent function name
>>> pos = nx.fruchterman_reingold_layout(G)
"""
import numpy as np
G, center = _process_params(G, center, dim)
if fixed is not None:
if pos is None:
raise ValueError("nodes are fixed without positions given")
for node in fixed:
if node not in pos:
raise ValueError("nodes are fixed without positions given")
nfixed = {node: i for i, node in enumerate(G)}
fixed = np.asarray([nfixed[node] for node in fixed if node in nfixed])
if pos is not None:
# Determine size of existing domain to adjust initial positions
dom_size = max(coord for pos_tup in pos.values() for coord in pos_tup)
if dom_size == 0:
dom_size = 1
pos_arr = seed.rand(len(G), dim) * dom_size + center
for i, n in enumerate(G):
if n in pos:
pos_arr[i] = np.asarray(pos[n])
else:
pos_arr = None
dom_size = 1
if len(G) == 0:
return {}
if len(G) == 1:
return {nx.utils.arbitrary_element(G.nodes()): center}
try:
# Sparse matrix
if len(G) < 500: # sparse solver for large graphs
raise ValueError
A = nx.to_scipy_sparse_array(G, weight=weight, dtype="f")
if k is None and fixed is not None:
# We must adjust k by domain size for layouts not near 1x1
nnodes, _ = A.shape
k = dom_size / np.sqrt(nnodes)
pos = _sparse_fruchterman_reingold(
A, k, pos_arr, fixed, iterations, threshold, dim, seed
)
except ValueError:
A = nx.to_numpy_array(G, weight=weight)
if k is None and fixed is not None:
# We must adjust k by domain size for layouts not near 1x1
nnodes, _ = A.shape
k = dom_size / np.sqrt(nnodes)
pos = _fruchterman_reingold(
A, k, pos_arr, fixed, iterations, threshold, dim, seed
)
if fixed is None and scale is not None:
pos = rescale_layout(pos, scale=scale) + center
pos = dict(zip(G, pos))
return pos
fruchterman_reingold_layout = spring_layout
@np_random_state(7)
def _fruchterman_reingold(
A, k=None, pos=None, fixed=None, iterations=50, threshold=1e-4, dim=2, seed=None
):
# Position nodes in adjacency matrix A using Fruchterman-Reingold
# Entry point for NetworkX graph is fruchterman_reingold_layout()
import numpy as np
try:
nnodes, _ = A.shape
except AttributeError as err:
msg = "fruchterman_reingold() takes an adjacency matrix as input"
raise nx.NetworkXError(msg) from err
if pos is None:
# random initial positions
pos = np.asarray(seed.rand(nnodes, dim), dtype=A.dtype)
else:
# make sure positions are of same type as matrix
pos = pos.astype(A.dtype)
# optimal distance between nodes
if k is None:
k = np.sqrt(1.0 / nnodes)
# the initial "temperature" is about .1 of domain area (=1x1)
# this is the largest step allowed in the dynamics.
# We need to calculate this in case our fixed positions force our domain
# to be much bigger than 1x1
t = max(max(pos.T[0]) - min(pos.T[0]), max(pos.T[1]) - min(pos.T[1])) * 0.1
# simple cooling scheme.
# linearly step down by dt on each iteration so last iteration is size dt.
dt = t / (iterations + 1)
delta = np.zeros((pos.shape[0], pos.shape[0], pos.shape[1]), dtype=A.dtype)
# the inscrutable (but fast) version
# this is still O(V^2)
# could use multilevel methods to speed this up significantly
for iteration in range(iterations):
# matrix of difference between points
delta = pos[:, np.newaxis, :] - pos[np.newaxis, :, :]
# distance between points
distance = np.linalg.norm(delta, axis=-1)
# enforce minimum distance of 0.01
np.clip(distance, 0.01, None, out=distance)
# displacement "force"
displacement = np.einsum(
"ijk,ij->ik", delta, (k * k / distance**2 - A * distance / k)
)
# update positions
length = np.linalg.norm(displacement, axis=-1)
length = np.where(length < 0.01, 0.1, length)
delta_pos = np.einsum("ij,i->ij", displacement, t / length)
if fixed is not None:
# don't change positions of fixed nodes
delta_pos[fixed] = 0.0
pos += delta_pos
# cool temperature
t -= dt
if (np.linalg.norm(delta_pos) / nnodes) < threshold:
break
return pos
@np_random_state(7)
def _sparse_fruchterman_reingold(
A, k=None, pos=None, fixed=None, iterations=50, threshold=1e-4, dim=2, seed=None
):
# Position nodes in adjacency matrix A using Fruchterman-Reingold
# Entry point for NetworkX graph is fruchterman_reingold_layout()
# Sparse version
import numpy as np
import scipy as sp
try:
nnodes, _ = A.shape
except AttributeError as err:
msg = "fruchterman_reingold() takes an adjacency matrix as input"
raise nx.NetworkXError(msg) from err
# make sure we have a LIst of Lists representation
try:
A = A.tolil()
except AttributeError:
A = (sp.sparse.coo_array(A)).tolil()
if pos is None:
# random initial positions
pos = np.asarray(seed.rand(nnodes, dim), dtype=A.dtype)
else:
# make sure positions are of same type as matrix
pos = pos.astype(A.dtype)
# no fixed nodes
if fixed is None:
fixed = []
# optimal distance between nodes
if k is None:
k = np.sqrt(1.0 / nnodes)
# the initial "temperature" is about .1 of domain area (=1x1)
# this is the largest step allowed in the dynamics.
t = max(max(pos.T[0]) - min(pos.T[0]), max(pos.T[1]) - min(pos.T[1])) * 0.1
# simple cooling scheme.
# linearly step down by dt on each iteration so last iteration is size dt.
dt = t / (iterations + 1)
displacement = np.zeros((dim, nnodes))
for iteration in range(iterations):
displacement *= 0
# loop over rows
for i in range(A.shape[0]):
if i in fixed:
continue
# difference between this row's node position and all others
delta = (pos[i] - pos).T
# distance between points
distance = np.sqrt((delta**2).sum(axis=0))
# enforce minimum distance of 0.01
distance = np.where(distance < 0.01, 0.01, distance)
# the adjacency matrix row
Ai = A.getrowview(i).toarray() # TODO: revisit w/ sparse 1D container
# displacement "force"
displacement[:, i] += (
delta * (k * k / distance**2 - Ai * distance / k)
).sum(axis=1)
# update positions
length = np.sqrt((displacement**2).sum(axis=0))
length = np.where(length < 0.01, 0.1, length)
delta_pos = (displacement * t / length).T
pos += delta_pos
# cool temperature
t -= dt
if (np.linalg.norm(delta_pos) / nnodes) < threshold:
break
return pos
[docs]
def kamada_kawai_layout(
G, dist=None, pos=None, weight="weight", scale=1, center=None, dim=2
):
"""Position nodes using Kamada-Kawai path-length cost-function.
Parameters
----------
G : NetworkX graph or list of nodes
A position will be assigned to every node in G.
dist : dict (default=None)
A two-level dictionary of optimal distances between nodes,
indexed by source and destination node.
If None, the distance is computed using shortest_path_length().
pos : dict or None optional (default=None)
Initial positions for nodes as a dictionary with node as keys
and values as a coordinate list or tuple. If None, then use
circular_layout() for dim >= 2 and a linear layout for dim == 1.
weight : string or None optional (default='weight')
The edge attribute that holds the numerical value used for
the edge weight. If None, then all edge weights are 1.
scale : number (default: 1)
Scale factor for positions.
center : array-like or None
Coordinate pair around which to center the layout.
dim : int
Dimension of layout.
Returns
-------
pos : dict
A dictionary of positions keyed by node
Examples
--------
>>> G = nx.path_graph(4)
>>> pos = nx.kamada_kawai_layout(G)
"""
import numpy as np
G, center = _process_params(G, center, dim)
nNodes = len(G)
if nNodes == 0:
return {}
if dist is None:
dist = dict(nx.shortest_path_length(G, weight=weight))
dist_mtx = 1e6 * np.ones((nNodes, nNodes))
for row, nr in enumerate(G):
if nr not in dist:
continue
rdist = dist[nr]
for col, nc in enumerate(G):
if nc not in rdist:
continue
dist_mtx[row][col] = rdist[nc]
if pos is None:
if dim >= 3:
pos = random_layout(G, dim=dim)
elif dim == 2:
pos = circular_layout(G, dim=dim)
else:
pos = dict(zip(G, np.linspace(0, 1, len(G))))
pos_arr = np.array([pos[n] for n in G])
pos = _kamada_kawai_solve(dist_mtx, pos_arr, dim)
pos = rescale_layout(pos, scale=scale) + center
return dict(zip(G, pos))
def _kamada_kawai_solve(dist_mtx, pos_arr, dim):
# Anneal node locations based on the Kamada-Kawai cost-function,
# using the supplied matrix of preferred inter-node distances,
# and starting locations.
import numpy as np
import scipy as sp
meanwt = 1e-3
costargs = (np, 1 / (dist_mtx + np.eye(dist_mtx.shape[0]) * 1e-3), meanwt, dim)
optresult = sp.optimize.minimize(
_kamada_kawai_costfn,
pos_arr.ravel(),
method="L-BFGS-B",
args=costargs,
jac=True,
)
return optresult.x.reshape((-1, dim))
def _kamada_kawai_costfn(pos_vec, np, invdist, meanweight, dim):
# Cost-function and gradient for Kamada-Kawai layout algorithm
nNodes = invdist.shape[0]
pos_arr = pos_vec.reshape((nNodes, dim))
delta = pos_arr[:, np.newaxis, :] - pos_arr[np.newaxis, :, :]
nodesep = np.linalg.norm(delta, axis=-1)
direction = np.einsum("ijk,ij->ijk", delta, 1 / (nodesep + np.eye(nNodes) * 1e-3))
offset = nodesep * invdist - 1.0
offset[np.diag_indices(nNodes)] = 0
cost = 0.5 * np.sum(offset**2)
grad = np.einsum("ij,ij,ijk->ik", invdist, offset, direction) - np.einsum(
"ij,ij,ijk->jk", invdist, offset, direction
)
# Additional parabolic term to encourage mean position to be near origin:
sumpos = np.sum(pos_arr, axis=0)
cost += 0.5 * meanweight * np.sum(sumpos**2)
grad += meanweight * sumpos
return (cost, grad.ravel())
[docs]
def spectral_layout(G, weight="weight", scale=1, center=None, dim=2):
"""Position nodes using the eigenvectors of the graph Laplacian.
Using the unnormalized Laplacian, the layout shows possible clusters of
nodes which are an approximation of the ratio cut. If dim is the number of
dimensions then the positions are the entries of the dim eigenvectors
corresponding to the ascending eigenvalues starting from the second one.
Parameters
----------
G : NetworkX graph or list of nodes
A position will be assigned to every node in G.
weight : string or None optional (default='weight')
The edge attribute that holds the numerical value used for
the edge weight. If None, then all edge weights are 1.
scale : number (default: 1)
Scale factor for positions.
center : array-like or None
Coordinate pair around which to center the layout.
dim : int
Dimension of layout.
Returns
-------
pos : dict
A dictionary of positions keyed by node
Examples
--------
>>> G = nx.path_graph(4)
>>> pos = nx.spectral_layout(G)
Notes
-----
Directed graphs will be considered as undirected graphs when
positioning the nodes.
For larger graphs (>500 nodes) this will use the SciPy sparse
eigenvalue solver (ARPACK).
"""
# handle some special cases that break the eigensolvers
import numpy as np
G, center = _process_params(G, center, dim)
if len(G) <= 2:
if len(G) == 0:
pos = np.array([])
elif len(G) == 1:
pos = np.array([center])
else:
pos = np.array([np.zeros(dim), np.array(center) * 2.0])
return dict(zip(G, pos))
try:
# Sparse matrix
if len(G) < 500: # dense solver is faster for small graphs
raise ValueError
A = nx.to_scipy_sparse_array(G, weight=weight, dtype="d")
# Symmetrize directed graphs
if G.is_directed():
A = A + np.transpose(A)
pos = _sparse_spectral(A, dim)
except (ImportError, ValueError):
# Dense matrix
A = nx.to_numpy_array(G, weight=weight)
# Symmetrize directed graphs
if G.is_directed():
A += A.T
pos = _spectral(A, dim)
pos = rescale_layout(pos, scale=scale) + center
pos = dict(zip(G, pos))
return pos
def _spectral(A, dim=2):
# Input adjacency matrix A
# Uses dense eigenvalue solver from numpy
import numpy as np
try:
nnodes, _ = A.shape
except AttributeError as err:
msg = "spectral() takes an adjacency matrix as input"
raise nx.NetworkXError(msg) from err
# form Laplacian matrix where D is diagonal of degrees
D = np.identity(nnodes, dtype=A.dtype) * np.sum(A, axis=1)
L = D - A
eigenvalues, eigenvectors = np.linalg.eig(L)
# sort and keep smallest nonzero
index = np.argsort(eigenvalues)[1 : dim + 1] # 0 index is zero eigenvalue
return np.real(eigenvectors[:, index])
def _sparse_spectral(A, dim=2):
# Input adjacency matrix A
# Uses sparse eigenvalue solver from scipy
# Could use multilevel methods here, see Koren "On spectral graph drawing"
import numpy as np
import scipy as sp
try:
nnodes, _ = A.shape
except AttributeError as err:
msg = "sparse_spectral() takes an adjacency matrix as input"
raise nx.NetworkXError(msg) from err
# form Laplacian matrix
# TODO: Rm csr_array wrapper in favor of spdiags array constructor when available
D = sp.sparse.csr_array(sp.sparse.spdiags(A.sum(axis=1), 0, nnodes, nnodes))
L = D - A
k = dim + 1
# number of Lanczos vectors for ARPACK solver.What is the right scaling?
ncv = max(2 * k + 1, int(np.sqrt(nnodes)))
# return smallest k eigenvalues and eigenvectors
eigenvalues, eigenvectors = sp.sparse.linalg.eigsh(L, k, which="SM", ncv=ncv)
index = np.argsort(eigenvalues)[1:k] # 0 index is zero eigenvalue
return np.real(eigenvectors[:, index])
[docs]
def planar_layout(G, scale=1, center=None, dim=2):
"""Position nodes without edge intersections.
Parameters
----------
G : NetworkX graph or list of nodes
A position will be assigned to every node in G. If G is of type
nx.PlanarEmbedding, the positions are selected accordingly.
scale : number (default: 1)
Scale factor for positions.
center : array-like or None
Coordinate pair around which to center the layout.
dim : int
Dimension of layout.
Returns
-------
pos : dict
A dictionary of positions keyed by node
Raises
------
NetworkXException
If G is not planar
Examples
--------
>>> G = nx.path_graph(4)
>>> pos = nx.planar_layout(G)
"""
import numpy as np
if dim != 2:
raise ValueError("can only handle 2 dimensions")
G, center = _process_params(G, center, dim)
if len(G) == 0:
return {}
if isinstance(G, nx.PlanarEmbedding):
embedding = G
else:
is_planar, embedding = nx.check_planarity(G)
if not is_planar:
raise nx.NetworkXException("G is not planar.")
pos = nx.combinatorial_embedding_to_pos(embedding)
node_list = list(embedding)
pos = np.vstack([pos[x] for x in node_list])
pos = pos.astype(np.float64)
pos = rescale_layout(pos, scale=scale) + center
return dict(zip(node_list, pos))
[docs]
def spiral_layout(G, scale=1, center=None, dim=2, resolution=0.35, equidistant=False):
"""Position nodes in a spiral layout.
Parameters
----------
G : NetworkX graph or list of nodes
A position will be assigned to every node in G.
scale : number (default: 1)
Scale factor for positions.
center : array-like or None
Coordinate pair around which to center the layout.
dim : int, default=2
Dimension of layout, currently only dim=2 is supported.
Other dimension values result in a ValueError.
resolution : float, default=0.35
The compactness of the spiral layout returned.
Lower values result in more compressed spiral layouts.
equidistant : bool, default=False
If True, nodes will be positioned equidistant from each other
by decreasing angle further from center.
If False, nodes will be positioned at equal angles
from each other by increasing separation further from center.
Returns
-------
pos : dict
A dictionary of positions keyed by node
Raises
------
ValueError
If dim != 2
Examples
--------
>>> G = nx.path_graph(4)
>>> pos = nx.spiral_layout(G)
>>> nx.draw(G, pos=pos)
Notes
-----
This algorithm currently only works in two dimensions.
"""
import numpy as np
if dim != 2:
raise ValueError("can only handle 2 dimensions")
G, center = _process_params(G, center, dim)
if len(G) == 0:
return {}
if len(G) == 1:
return {nx.utils.arbitrary_element(G): center}
pos = []
if equidistant:
chord = 1
step = 0.5
theta = resolution
theta += chord / (step * theta)
for _ in range(len(G)):
r = step * theta
theta += chord / r
pos.append([np.cos(theta) * r, np.sin(theta) * r])
else:
dist = np.arange(len(G), dtype=float)
angle = resolution * dist
pos = np.transpose(dist * np.array([np.cos(angle), np.sin(angle)]))
pos = rescale_layout(np.array(pos), scale=scale) + center
pos = dict(zip(G, pos))
return pos
[docs]
def multipartite_layout(G, subset_key="subset", align="vertical", scale=1, center=None):
"""Position nodes in layers of straight lines.
Parameters
----------
G : NetworkX graph or list of nodes
A position will be assigned to every node in G.
subset_key : string or dict (default='subset')
If a string, the key of node data in G that holds the node subset.
If a dict, keyed by layer number to the nodes in that layer/subset.
align : string (default='vertical')
The alignment of nodes. Vertical or horizontal.
scale : number (default: 1)
Scale factor for positions.
center : array-like or None
Coordinate pair around which to center the layout.
Returns
-------
pos : dict
A dictionary of positions keyed by node.
Examples
--------
>>> G = nx.complete_multipartite_graph(28, 16, 10)
>>> pos = nx.multipartite_layout(G)
or use a dict to provide the layers of the layout
>>> G = nx.Graph([(0, 1), (1, 2), (1, 3), (3, 4)])
>>> layers = {"a": [0], "b": [1], "c": [2, 3], "d": [4]}
>>> pos = nx.multipartite_layout(G, subset_key=layers)
Notes
-----
This algorithm currently only works in two dimensions and does not
try to minimize edge crossings.
Network does not need to be a complete multipartite graph. As long as nodes
have subset_key data, they will be placed in the corresponding layers.
"""
import numpy as np
if align not in ("vertical", "horizontal"):
msg = "align must be either vertical or horizontal."
raise ValueError(msg)
G, center = _process_params(G, center=center, dim=2)
if len(G) == 0:
return {}
try:
# check if subset_key is dict-like
if len(G) != sum(len(nodes) for nodes in subset_key.values()):
raise nx.NetworkXError(
"all nodes must be in one subset of `subset_key` dict"
)
except AttributeError:
# subset_key is not a dict, hence a string
node_to_subset = nx.get_node_attributes(G, subset_key)
if len(node_to_subset) != len(G):
raise nx.NetworkXError(
f"all nodes need a subset_key attribute: {subset_key}"
)
subset_key = nx.utils.groups(node_to_subset)
# Sort by layer, if possible
try:
layers = dict(sorted(subset_key.items()))
except TypeError:
layers = subset_key
pos = None
nodes = []
width = len(layers)
for i, layer in enumerate(layers.values()):
height = len(layer)
xs = np.repeat(i, height)
ys = np.arange(0, height, dtype=float)
offset = ((width - 1) / 2, (height - 1) / 2)
layer_pos = np.column_stack([xs, ys]) - offset
if pos is None:
pos = layer_pos
else:
pos = np.concatenate([pos, layer_pos])
nodes.extend(layer)
pos = rescale_layout(pos, scale=scale) + center
if align == "horizontal":
pos = pos[:, ::-1] # swap x and y coords
pos = dict(zip(nodes, pos))
return pos
[docs]
@np_random_state("seed")
def arf_layout(
G,
pos=None,
scaling=1,
a=1.1,
etol=1e-6,
dt=1e-3,
max_iter=1000,
*,
seed=None,
):
"""Arf layout for networkx
The attractive and repulsive forces (arf) layout [1]
improves the spring layout in three ways. First, it
prevents congestion of highly connected nodes due to
strong forcing between nodes. Second, it utilizes the
layout space more effectively by preventing large gaps
that spring layout tends to create. Lastly, the arf
layout represents symmetries in the layout better than
the default spring layout.
Parameters
----------
G : nx.Graph or nx.DiGraph
Networkx graph.
pos : dict
Initial position of the nodes. If set to None a
random layout will be used.
scaling : float
Scales the radius of the circular layout space.
a : float
Strength of springs between connected nodes. Should be larger than 1. The greater a, the clearer the separation ofunconnected sub clusters.
etol : float
Gradient sum of spring forces must be larger than `etol` before successful termination.
dt : float
Time step for force differential equation simulations.
max_iter : int
Max iterations before termination of the algorithm.
seed : int, RandomState instance or None optional (default=None)
Set the random state for deterministic node layouts.
If int, `seed` is the seed used by the random number generator,
if numpy.random.RandomState instance, `seed` is the random
number generator,
if None, the random number generator is the RandomState instance used
by numpy.random.
References
.. [1] "Self-Organization Applied to Dynamic Network Layout", M. Geipel,
International Journal of Modern Physics C, 2007, Vol 18, No 10, pp. 1537-1549.
https://doi.org/10.1142/S0129183107011558 https://arxiv.org/abs/0704.1748
Returns
-------
pos : dict
A dictionary of positions keyed by node.
Examples
--------
>>> G = nx.grid_graph((5, 5))
>>> pos = nx.arf_layout(G)
"""
import warnings
import numpy as np
if a <= 1:
msg = "The parameter a should be larger than 1"
raise ValueError(msg)
pos_tmp = nx.random_layout(G, seed=seed)
if pos is None:
pos = pos_tmp
else:
for node in G.nodes():
if node not in pos:
pos[node] = pos_tmp[node].copy()
# Initialize spring constant matrix
N = len(G)
# No nodes no computation
if N == 0:
return pos
# init force of springs
K = np.ones((N, N)) - np.eye(N)
node_order = {node: i for i, node in enumerate(G)}
for x, y in G.edges():
if x != y:
idx, jdx = (node_order[i] for i in (x, y))
K[idx, jdx] = a
# vectorize values
p = np.asarray(list(pos.values()))
# equation 10 in [1]
rho = scaling * np.sqrt(N)
# looping variables
error = etol + 1
n_iter = 0
while error > etol:
diff = p[:, np.newaxis] - p[np.newaxis]
A = np.linalg.norm(diff, axis=-1)[..., np.newaxis]
# attraction_force - repulsions force
# suppress nans due to division; caused by diagonal set to zero.
# Does not affect the computation due to nansum
with warnings.catch_warnings():
warnings.simplefilter("ignore")
change = K[..., np.newaxis] * diff - rho / A * diff
change = np.nansum(change, axis=0)
p += change * dt
error = np.linalg.norm(change, axis=-1).sum()
if n_iter > max_iter:
break
n_iter += 1
return dict(zip(G.nodes(), p))
[docs]
@np_random_state("seed")
def forceatlas2_layout(
G,
pos=None,
*,
max_iter=100,
jitter_tolerance=1.0,
scaling_ratio=2.0,
gravity=1.0,
distributed_action=False,
strong_gravity=False,
node_mass=None,
node_size=None,
weight=None,
dissuade_hubs=False,
linlog=False,
seed=None,
dim=2,
):
"""Position nodes using the ForceAtlas2 force-directed layout algorithm.
This function applies the ForceAtlas2 layout algorithm [1]_ to a NetworkX graph,
positioning the nodes in a way that visually represents the structure of the graph.
The algorithm uses physical simulation to minimize the energy of the system,
resulting in a more readable layout.
Parameters
----------
G : nx.Graph
A NetworkX graph to be laid out.
pos : dict or None, optional
Initial positions of the nodes. If None, random initial positions are used.
max_iter : int (default: 100)
Number of iterations for the layout optimization.
jitter_tolerance : float (default: 1.0)
Controls the tolerance for adjusting the speed of layout generation.
scaling_ratio : float (default: 2.0)
Determines the scaling of attraction and repulsion forces.
distributed_attraction : bool (default: False)
Distributes the attraction force evenly among nodes.
strong_gravity : bool (default: False)
Applies a strong gravitational pull towards the center.
node_mass : dict or None, optional
Maps nodes to their masses, influencing the attraction to other nodes.
node_size : dict or None, optional
Maps nodes to their sizes, preventing crowding by creating a halo effect.
dissuade_hubs : bool (default: False)
Prevents the clustering of hub nodes.
linlog : bool (default: False)
Uses logarithmic attraction instead of linear.
seed : int, RandomState instance or None optional (default=None)
Used only for the initial positions in the algorithm.
Set the random state for deterministic node layouts.
If int, `seed` is the seed used by the random number generator,
if numpy.random.RandomState instance, `seed` is the random
number generator,
if None, the random number generator is the RandomState instance used
by numpy.random.
dim : int (default: 2)
Sets the dimensions for the layout. Ignored if `pos` is provided.
Examples
--------
>>> import networkx as nx
>>> G = nx.florentine_families_graph()
>>> pos = nx.forceatlas2_layout(G)
>>> nx.draw(G, pos=pos)
References
----------
.. [1] Jacomy, M., Venturini, T., Heymann, S., & Bastian, M. (2014).
ForceAtlas2, a continuous graph layout algorithm for handy network
visualization designed for the Gephi software. PloS one, 9(6), e98679.
https://doi.org/10.1371/journal.pone.0098679
"""
import numpy as np
if len(G) == 0:
return {}
# parse optional pos positions
if pos is None:
pos = nx.random_layout(G, dim=dim, seed=seed)
pos_arr = np.array(list(pos.values()))
else:
# set default node interval within the initial pos values
pos_init = np.array(list(pos.values()))
max_pos = pos_init.max(axis=0)
min_pos = pos_init.min(axis=0)
dim = max_pos.size
pos_arr = min_pos + seed.rand(len(G), dim) * (max_pos - min_pos)
for idx, node in enumerate(G):
if node in pos:
pos_arr[idx] = pos[node].copy()
mass = np.zeros(len(G))
size = np.zeros(len(G))
# Only adjust for size when the users specifies size other than default (1)
adjust_sizes = False
if node_size is None:
node_size = {}
else:
adjust_sizes = True
if node_mass is None:
node_mass = {}
for idx, node in enumerate(G):
mass[idx] = node_mass.get(node, G.degree(node) + 1)
size[idx] = node_size.get(node, 1)
n = len(G)
gravities = np.zeros((n, dim))
attraction = np.zeros((n, dim))
repulsion = np.zeros((n, dim))
A = nx.to_numpy_array(G, weight=weight)
def estimate_factor(n, swing, traction, speed, speed_efficiency, jitter_tolerance):
"""Computes the scaling factor for the force in the ForceAtlas2 layout algorithm.
This helper function adjusts the speed and
efficiency of the layout generation based on the
current state of the system, such as the number of
nodes, current swing, and traction forces.
Parameters
----------
n : int
Number of nodes in the graph.
swing : float
The current swing, representing the oscillation of the nodes.
traction : float
The current traction force, representing the attraction between nodes.
speed : float
The current speed of the layout generation.
speed_efficiency : float
The efficiency of the current speed, influencing how fast the layout converges.
jitter_tolerance : float
The tolerance for jitter, affecting how much speed adjustment is allowed.
Returns
-------
tuple
A tuple containing the updated speed and speed efficiency.
Notes
-----
This function is a part of the ForceAtlas2 layout algorithm and is used to dynamically adjust the
layout parameters to achieve an optimal and stable visualization.
"""
import numpy as np
# estimate jitter
opt_jitter = 0.05 * np.sqrt(n)
min_jitter = np.sqrt(opt_jitter)
max_jitter = 10
min_speed_efficiency = 0.05
other = min(max_jitter, opt_jitter * traction / n**2)
jitter = jitter_tolerance * max(min_jitter, other)
if swing / traction > 2.0:
if speed_efficiency > min_speed_efficiency:
speed_efficiency *= 0.5
jitter = max(jitter, jitter_tolerance)
if swing == 0:
target_speed = np.inf
else:
target_speed = jitter * speed_efficiency * traction / swing
if swing > jitter * traction:
if speed_efficiency > min_speed_efficiency:
speed_efficiency *= 0.7
elif speed < 1000:
speed_efficiency *= 1.3
max_rise = 0.5
speed = speed + min(target_speed - speed, max_rise * speed)
return speed, speed_efficiency
speed = 1
speed_efficiency = 1
swing = 1
traction = 1
for _ in range(max_iter):
# compute pairwise difference
diff = pos_arr[:, None] - pos_arr[None]
# compute pairwise distance
distance = np.linalg.norm(diff, axis=-1)
# linear attraction
if linlog:
attraction = -np.log(1 + distance) / distance
np.fill_diagonal(attraction, 0)
attraction = np.einsum("ij, ij -> ij", attraction, A)
attraction = np.einsum("ijk, ij -> ik", diff, attraction)
else:
attraction = -np.einsum("ijk, ij -> ik", diff, A)
if distributed_action:
attraction /= mass[:, None]
# repulsion
tmp = mass[:, None] @ mass[None]
if adjust_sizes:
distance += -size[:, None] - size[None]
d2 = distance**2
# remove self-interaction
np.fill_diagonal(tmp, 0)
np.fill_diagonal(d2, 1)
factor = (tmp / d2) * scaling_ratio
repulsion = np.einsum("ijk, ij -> ik", diff, factor)
# gravity
gravities = (
-gravity
* mass[:, None]
* pos_arr
/ np.linalg.norm(pos_arr, axis=-1)[:, None]
)
if strong_gravity:
gravities *= np.linalg.norm(pos_arr, axis=-1)[:, None]
# total forces
update = attraction + repulsion + gravities
# compute total swing and traction
swing += (mass * np.linalg.norm(pos_arr - update, axis=-1)).sum()
traction += (0.5 * mass * np.linalg.norm(pos_arr + update, axis=-1)).sum()
speed, speed_efficiency = estimate_factor(
n,
swing,
traction,
speed,
speed_efficiency,
jitter_tolerance,
)
# update pos
if adjust_sizes:
swinging = mass * np.linalg.norm(update, axis=-1)
factor = 0.1 * speed / (1 + np.sqrt(speed * swinging))
df = np.linalg.norm(update, axis=-1)
factor = np.minimum(factor * df, 10.0 * np.ones(df.shape)) / df
else:
swinging = mass * np.linalg.norm(update, axis=-1)
factor = speed / (1 + np.sqrt(speed * swinging))
pos_arr += update * factor[:, None]
if abs((update * factor[:, None]).sum()) < 1e-10:
break
return dict(zip(G, pos_arr))
[docs]
def rescale_layout(pos, scale=1):
"""Returns scaled position array to (-scale, scale) in all axes.
The function acts on NumPy arrays which hold position information.
Each position is one row of the array. The dimension of the space
equals the number of columns. Each coordinate in one column.
To rescale, the mean (center) is subtracted from each axis separately.
Then all values are scaled so that the largest magnitude value
from all axes equals `scale` (thus, the aspect ratio is preserved).
The resulting NumPy Array is returned (order of rows unchanged).
Parameters
----------
pos : numpy array
positions to be scaled. Each row is a position.
scale : number (default: 1)
The size of the resulting extent in all directions.
Returns
-------
pos : numpy array
scaled positions. Each row is a position.
See Also
--------
rescale_layout_dict
"""
import numpy as np
# Find max length over all dimensions
pos -= pos.mean(axis=0)
lim = np.abs(pos).max() # max coordinate for all axes
# rescale to (-scale, scale) in all directions, preserves aspect
if lim > 0:
pos *= scale / lim
return pos
[docs]
def rescale_layout_dict(pos, scale=1):
"""Return a dictionary of scaled positions keyed by node
Parameters
----------
pos : A dictionary of positions keyed by node
scale : number (default: 1)
The size of the resulting extent in all directions.
Returns
-------
pos : A dictionary of positions keyed by node
Examples
--------
>>> import numpy as np
>>> pos = {0: np.array((0, 0)), 1: np.array((1, 1)), 2: np.array((0.5, 0.5))}
>>> nx.rescale_layout_dict(pos)
{0: array([-1., -1.]), 1: array([1., 1.]), 2: array([0., 0.])}
>>> pos = {0: np.array((0, 0)), 1: np.array((-1, 1)), 2: np.array((-0.5, 0.5))}
>>> nx.rescale_layout_dict(pos, scale=2)
{0: array([ 2., -2.]), 1: array([-2., 2.]), 2: array([0., 0.])}
See Also
--------
rescale_layout
"""
import numpy as np
if not pos: # empty_graph
return {}
pos_v = np.array(list(pos.values()))
pos_v = rescale_layout(pos_v, scale=scale)
return dict(zip(pos, pos_v))
[docs]
def bfs_layout(G, start, *, align="vertical", scale=1, center=None):
"""Position nodes according to breadth-first search algorithm.
Parameters
----------
G : NetworkX graph
A position will be assigned to every node in G.
start : node in `G`
Starting node for bfs
center : array-like or None
Coordinate pair around which to center the layout.
Returns
-------
pos : dict
A dictionary of positions keyed by node.
Examples
--------
>>> G = nx.path_graph(4)
>>> pos = nx.bfs_layout(G, 0)
Notes
-----
This algorithm currently only works in two dimensions and does not
try to minimize edge crossings.
"""
G, center = _process_params(G, center, 2)
# Compute layers with BFS
layers = dict(enumerate(nx.bfs_layers(G, start)))
if len(G) != sum(len(nodes) for nodes in layers.values()):
raise nx.NetworkXError(
"bfs_layout didn't include all nodes. Perhaps use input graph:\n"
" G.subgraph(nx.node_connected_component(G, start))"
)
# Compute node positions with multipartite_layout
return multipartite_layout(
G, subset_key=layers, align=align, scale=scale, center=center
)
