def setUp(self):
self.louvain = Louvain(engine='python')
self.bilouvain = BiLouvain(engine='python')
if is_numba_available:
self.louvain_numba = Louvain(engine='numba')
self.bilouvain_numba = BiLouvain(engine='numba')
else:
with self.assertRaises(ValueError):
Louvain(engine='numba')
def test_bilouvain(self):
biadjacency = star_wars()
adjacency = bipartite2undirected(biadjacency)
louvain = Louvain(modularity='newman')
bilouvain = BiLouvain(modularity='newman')
labels1 = louvain.fit_transform(adjacency)
bilouvain.fit(biadjacency)
labels2 = np.concatenate((bilouvain.labels_row_, bilouvain.labels_col_))
self.assertTrue((labels1 == labels2).all())
def fit_predict(self, base_clusters, modal_graphs):
ba_matrices =[]
idxs = []
idxs_iter = 0
if isinstance(clusters, pd.DataFrame):
clusters = [clusters.loc[:,i].to_numpy(dtype=int) for i in clusters.columns]
else:
clusters = [clustering.astype(np.int64) for clustering in clusters]
for base_cluster in base_clusters:
ba_matrix = np.zeros((base_cluster.size, base_cluster.max()+1))
ba_matrix[np.arange(base_cluster.size), base_cluster] = 1
ba_matrices.append(ba_matrix)
idxs.append([idxs_iter, idxs_iter+ba_matrix.shape[1]])
idxs_iter += ba_matrix.shape[1]
ba_matrix = np.concatenate(ba_matrices, axis=1)
for G in modal_graphs:
self.W.append(normalize(csr_matrix(G).T, norm='l1', axis=1, copy=True))
ca_matrix = ba_matrix.copy()
for t in range(self.iterations):
temp = []
for G_m in self.W:
temp.append(self.alpha * G_m @ ca_matrix + (1-self.alpha)* ba_matrix )
ca_matrix = np.mean(temp, axis=0)
self._ca_matrix = ca_matrix
clstr = BiLouvain()
clstr.fit(self._ca_matrix)
self._object_labels = clstr.row_labels_
self._cluster_labels = clstr.col_labels_
self._quality = bimodularity(self._ca_matrix, self._object_labels,
self._cluster_labels)
return self._object_labels
def svg_bigraph(biadjacency: sparse.csr_matrix,
names_row: Optional[np.ndarray] = None, names_col: Optional[np.ndarray] = None,
labels_row: Optional[Union[dict, np.ndarray]] = None,
labels_col: Optional[Union[dict, np.ndarray]] = None,
scores_row: Optional[Union[dict, np.ndarray]] = None,
scores_col: Optional[Union[dict, np.ndarray]] = None,
membership_row: Optional[sparse.csr_matrix] = None,
membership_col: Optional[sparse.csr_matrix] = None,
seeds_row: Union[list, dict] = None, seeds_col: Union[list, dict] = None,
position_row: Optional[np.ndarray] = None, position_col: Optional[np.ndarray] = None,
reorder: bool = True, width: Optional[float] = 400,
height: Optional[float] = 300, margin: float = 20, margin_text: float = 3, scale: float = 1,
node_size: float = 7, node_size_min: float = 1, node_size_max: float = 20,
display_node_weight: bool = False,
node_weights_row: Optional[np.ndarray] = None, node_weights_col: Optional[np.ndarray] = None,
node_width: float = 1, node_width_max: float = 3,
color_row: str = 'gray', color_col: str = 'gray', label_colors: Optional[Iterable] = None,
display_edges: bool = True, edge_labels: Optional[list] = None, edge_width: float = 1,
edge_width_min: float = 0.5, edge_width_max: float = 10, edge_color: str = 'black',
display_edge_weight: bool = True,
font_size: int = 12, filename: Optional[str] = None) -> str:
"""Return SVG image of a bigraph.
Parameters
----------
biadjacency :
Biadjacency matrix of the graph.
names_row :
Names of the rows.
names_col :
Names of the columns.
labels_row :
Labels of the rows (negative values mean no label).
labels_col :
Labels of the columns (negative values mean no label).
scores_row :
Scores of the rows (measure of importance).
scores_col :
Scores of the columns (measure of importance).
membership_row :
Membership of the rows (label distribution).
membership_col :
Membership of the columns (label distribution).
seeds_row :
Rows to be highlighted (if dict, only keys are considered).
seeds_col :
Columns to be highlighted (if dict, only keys are considered).
position_row :
Positions of the rows.
position_col :
Positions of the columns.
reorder :
Use clustering to order nodes.
width :
Width of the image.
height :
Height of the image.
margin :
Margin of the image.
margin_text :
Margin between node and text.
scale :
Multiplicative factor on the dimensions of the image.
node_size :
Size of nodes.
node_size_min :
Minimum size of nodes.
node_size_max :
Maximum size of nodes.
display_node_weight :
If ``True``, display node weights through node size.
node_weights_row :
Weights of rows (used only if **display_node_weight** is ``True``).
node_weights_col :
Weights of columns (used only if **display_node_weight** is ``True``).
node_width :
Width of node circle.
node_width_max :
Maximum width of node circle.
color_row :
Default color of rows (svg color).
color_col :
Default color of cols (svg color).
label_colors :
Colors of the labels (svg color).
display_edges :
If ``True``, display edges.
edge_labels :
Labels of the edges, as a list of tuples (source, destination, label)
edge_width :
Width of edges.
edge_width_min :
Minimum width of edges.
edge_width_max :
Maximum width of edges.
display_edge_weight :
If ``True``, display edge weights through edge widths.
edge_color :
Default color of edges (svg color).
font_size :
Font size.
filename :
Filename for saving image (optional).
Returns
-------
image : str
SVG image.
Example
-------
>>> from sknetwork.data import movie_actor
>>> biadjacency = movie_actor()
>>> from sknetwork.visualization import svg_bigraph
>>> image = svg_bigraph(biadjacency)
>>> image[1:4]
'svg'
"""
n_row, n_col = biadjacency.shape
# node positions
if position_row is None or position_col is None:
position_row = np.zeros((n_row, 2))
position_col = np.ones((n_col, 2))
if reorder:
bilouvain = BiLouvain()
bilouvain.fit(biadjacency)
index_row = np.argsort(bilouvain.labels_row_)
index_col = np.argsort(bilouvain.labels_col_)
else:
index_row = np.arange(n_row)
index_col = np.arange(n_col)
position_row[index_row, 1] = np.arange(n_row)
position_col[index_col, 1] = np.arange(n_col) + .5 * (n_row - n_col)
position = np.vstack((position_row, position_col))
# node colors
colors_row = get_node_colors(n_row, labels_row, scores_row, membership_row, color_row, label_colors)
colors_col = get_node_colors(n_col, labels_col, scores_col, membership_col, color_col, label_colors)
# node sizes
if node_weights_row is None:
node_weights_row = biadjacency.dot(np.ones(n_col))
if node_weights_col is None:
node_weights_col = biadjacency.T.dot(np.ones(n_row))
node_sizes_row, node_sizes_col = get_node_sizes_bipartite(node_weights_row, node_weights_col,
node_size, node_size_min, node_size_max,
display_node_weight)
# node widths
node_widths_row = get_node_widths(n_row, seeds_row, node_width, node_width_max)
node_widths_col = get_node_widths(n_col, seeds_col, node_width, node_width_max)
# rescaling
if not width and not height:
raise ValueError("You must specify either the width or the height of the image.")
position, width, height = rescale(position, width, height, margin, node_size, node_size_max, display_node_weight)
# node names
if names_row is not None:
text_length = np.max(np.array([len(str(name)) for name in names_row]))
position[:, 0] += text_length * font_size * .5
width += text_length * font_size * .5
if names_col is not None:
text_length = np.max(np.array([len(str(name)) for name in names_col]))
width += text_length * font_size * .5
# scaling
position *= scale
height *= scale
width *= scale
position_row = position[:n_row]
position_col = position[n_row:]
svg = """<svg width="{}" height="{}" xmlns="http://www.w3.org/2000/svg">\n""".format(width, height)
# edges
if display_edges:
biadjacency_coo = sparse.coo_matrix(biadjacency)
if edge_color is None:
if names_row is None and names_col is None:
edge_color = 'black'
else:
edge_color = 'gray'
edge_colors, edge_order, edge_colors_residual = get_edge_colors(biadjacency, edge_labels, edge_color,
label_colors)
edge_widths = get_edge_widths(biadjacency_coo, edge_width, edge_width_min, edge_width_max, display_edge_weight)
for ix in edge_order:
i = biadjacency_coo.row[ix]
j = biadjacency_coo.col[ix]
color = edge_colors[ix]
svg += svg_edge(pos_1=position_row[i], pos_2=position_col[j], edge_width=edge_widths[ix], edge_color=color)
for i, j, color in edge_colors_residual:
svg += svg_edge(pos_1=position_row[i], pos_2=position_col[j], edge_width=edge_width, edge_color=color)
# nodes
for i in range(n_row):
if membership_row is None:
svg += svg_node(position_row[i], node_sizes_row[i], colors_row[i], node_widths_row[i])
else:
if membership_row[i].nnz == 1:
index = membership_row[i].indices[0]
svg += svg_node(position_row[i], node_sizes_row[i], colors_row[index], node_widths_row[i])
else:
svg += svg_pie_chart_node(position_row[i], node_sizes_row[i], membership_row[i].todense(),
colors_row, node_widths_row[i])
for i in range(n_col):
if membership_col is None:
svg += svg_node(position_col[i], node_sizes_col[i], colors_col[i], node_widths_col[i])
else:
if membership_col[i].nnz == 1:
index = membership_col[i].indices[0]
svg += svg_node(position_col[i], node_sizes_col[i], colors_col[index], node_widths_col[i])
else:
svg += svg_pie_chart_node(position_col[i], node_sizes_col[i], membership_col[i].todense(),
colors_col, node_widths_col[i])
# text
if names_row is not None:
for i in range(n_row):
svg += svg_text(position_row[i] - (margin_text + node_sizes_row[i], 0), names_row[i], font_size, True)
if names_col is not None:
for i in range(n_col):
svg += svg_text(position_col[i] + (margin_text + node_sizes_col[i], 0), names_col[i], font_size)
svg += """</svg>\n"""
if filename is not None:
with open(filename + '.svg', 'w') as f:
f.write(svg)
return svg