scikit-network 0.33.3__cp313-cp313-macosx_10_13_x86_64.whl

sknetwork/visualization/graphs.py

@@ -0,0 +1,1039 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created in April 2020
+@author: Thomas Bonald <thomas.bonald@telecom-paris.fr>
+@author: Quentin Lutz <qlutz@live.fr>
+"""
+from typing import Optional, Iterable, Union, Tuple
+
+import numpy as np
+from scipy import sparse
+
+from sknetwork.clustering.louvain import Louvain
+from sknetwork.utils.format import is_symmetric, check_format
+from sknetwork.embedding.spring import Spring
+from sknetwork.visualization.colors import STANDARD_COLORS, COOLWARM_RGB
+
+
+def min_max_scaling(x: np.ndarray, x_min: Optional[float] = None, x_max: Optional[float] = None) -> np.ndarray:
+    """Shift and scale vector to be between 0 and 1."""
+    x = x.astype(float)
+    if x_min is None:
+        x_min = np.min(x)
+    if x_max is None:
+        x_max = np.max(x)
+    x -= x_min
+    if x_max > x_min:
+        x /= (x_max - x_min)
+    else:
+        x = .5 * np.ones_like(x)
+    return x
+
+
+def rescale(position: np.ndarray, width: float, height: float, margin: float, node_size: float, node_size_max: float,
+            display_node_weight: bool, names: Optional[np.ndarray] = None, name_position: str = 'right',
+            font_size: int = 12):
+    """Rescale position and adjust parameters.
+
+    Parameters
+    ----------
+    position :
+        array to rescale
+    width :
+        Horizontal scaling parameter
+    height :
+        Vertical scaling parameter
+    margin :
+        Minimal margin for the plot
+    node_size :
+        Node size (used to adapt the margin)
+    node_size_max :
+        Maximum node size (used to adapt the margin)
+    display_node_weight :
+        If ``True``, display node weight (used to adapt the margin)
+    names :
+        Names of nodes.
+    name_position :
+        Position of names (left, right, above, below)
+    font_size :
+        Font size
+
+    Returns
+    -------
+    position :
+        Rescaled positions
+    width :
+        Rescaled width
+    height :
+        Rescaled height
+    """
+    x = position[:, 0]
+    y = position[:, 1]
+    span_x = np.max(x) - np.min(x)
+    span_y = np.max(y) - np.min(y)
+    x = min_max_scaling(x)
+    y = 1 - min_max_scaling(y)
+    position = np.vstack((x, y)).T
+
+    # rescale
+    if width and not height:
+        height = width
+        if span_x and span_y:
+            height *= span_y / span_x
+    elif height and not width:
+        width = height
+        if span_x and span_y:
+            width *= span_x / span_y
+    position = position * np.array([width, height])
+
+    # text
+    if names is not None:
+        lengths = np.array([len(str(name)) for name in names])
+        if name_position == 'left':
+            margin_left = -np.min(position[:, 0] - lengths * font_size)
+            margin_left = margin_left * (margin_left > 0)
+            position[:, 0] += margin_left
+            width += margin_left
+        elif name_position == 'right':
+            margin_right = np.max(position[:, 0] + lengths * font_size - width)
+            margin_right = margin_right * (margin_right > 0)
+            width += margin_right
+        else:
+            margin_left = -np.min(position[:, 0] - lengths * font_size / 2)
+            margin_left = margin_left * (margin_left > 0)
+            margin_right = np.max(position[:, 0] + lengths * font_size / 2 - width)
+            margin_right = margin_right * (margin_right > 0)
+            position[:, 0] += margin_left
+            width += margin_left + margin_right
+            if name_position == 'above':
+                position[:, 1] += font_size
+                height += font_size
+            else:
+                height += font_size
+
+    # margins
+    margin = max(margin, node_size_max * display_node_weight, node_size)
+    position += margin
+    width += 2 * margin
+    height += 2 * margin
+    return position, width, height
+
+
+def get_label_colors(label_colors: Optional[Iterable]):
+    """Return label svg colors.
+
+    Examples
+    --------
+    >>> get_label_colors(['black'])
+    array(['black'], dtype='<U5')
+    >>> get_label_colors({0: 'blue'})
+    array(['blue'], dtype='<U64')
+    """
+    if label_colors is not None:
+        if isinstance(label_colors, dict):
+            keys = list(label_colors.keys())
+            values = list(label_colors.values())
+            label_colors = np.array(['black'] * (max(keys) + 1), dtype='U64')
+            label_colors[keys] = values
+        elif isinstance(label_colors, list):
+            label_colors = np.array(label_colors)
+    else:
+        label_colors = STANDARD_COLORS.copy()
+    return label_colors
+
+
+def get_node_colors(n: int, labels: Optional[Iterable], scores: Optional[Iterable],
+                    membership: Optional[sparse.csr_matrix],
+                    node_color: str, label_colors: Optional[Iterable],
+                    score_min: Optional[float] = None, score_max: Optional[float] = None) -> np.ndarray:
+    """Return the colors of the nodes using either labels or scores or default color."""
+    node_colors = np.array(n * [node_color]).astype('U64')
+    if labels is not None:
+        if isinstance(labels, dict):
+            keys = np.array(list(labels.keys()))
+            values = np.array(list(labels.values())).astype(int)
+            labels = -np.ones(n, dtype=int)
+            labels[keys] = values
+        elif isinstance(labels, list):
+            if len(labels) != n:
+                raise ValueError("The number of labels must be equal to the corresponding number of nodes.")
+            else:
+                labels = np.array(labels)
+        index = labels >= 0
+        label_colors = get_label_colors(label_colors)
+        node_colors[index] = label_colors[labels[index] % len(label_colors)]
+    elif scores is not None:
+        colors_score = COOLWARM_RGB.copy()
+        n_colors = colors_score.shape[0]
+        colors_score_svg = np.array(['rgb' + str(tuple([int(c) for c in colors_score[i]])) for i in range(n_colors)])
+        if isinstance(scores, dict):
+            keys = np.array(list(scores.keys()))
+            values = np.array(list(scores.values()))
+            scores = (min_max_scaling(values, score_min, score_max) * (n_colors - 1)).astype(int)
+            node_colors[keys] = colors_score_svg[scores]
+        else:
+            if isinstance(scores, list):
+                if len(scores) != n:
+                    raise ValueError("The number of scores must be equal to the corresponding number of nodes.")
+                else:
+                    scores = np.array(scores)
+            scores = (min_max_scaling(scores, score_min, score_max) * (n_colors - 1)).astype(int)
+            node_colors = colors_score_svg[scores]
+    elif membership is not None:
+        if isinstance(label_colors, dict):
+            raise TypeError("Label colors must be a list or an array when using a membership.")
+        label_colors = get_label_colors(label_colors)
+        node_colors = label_colors
+    return node_colors
+
+
+def get_node_widths(n: int, seeds: Union[int, dict, list], node_width: float, node_width_max: float) -> np.ndarray:
+    """Return the node widths."""
+    node_widths = node_width * np.ones(n)
+    if seeds is not None:
+        if type(seeds) == dict:
+            seeds = list(seeds.keys())
+        elif np.issubdtype(type(seeds), np.integer):
+            seeds = [seeds]
+        if len(seeds):
+            node_widths[np.array(seeds)] = node_width_max
+    return node_widths
+
+
+def get_node_sizes(weights: np.ndarray, node_size: float, node_size_min: float, node_size_max: float, node_weight) \
+        -> np.ndarray:
+    """Return the node sizes."""
+    if node_weight and np.min(weights) < np.max(weights):
+        node_sizes = node_size_min + np.abs(node_size_max - node_size_min) * weights / np.max(weights)
+    else:
+        node_sizes = node_size * np.ones_like(weights)
+    return node_sizes
+
+
+def get_node_sizes_bipartite(weights_row: np.ndarray, weights_col: np.ndarray, node_size: float, node_size_min: float,
+                             node_size_max: float, node_weight) -> (np.ndarray, np.ndarray):
+    """Return the node sizes for bipartite graphs."""
+    weights = np.hstack((weights_row, weights_col))
+    if node_weight and np.min(weights) < np.max(weights):
+        node_sizes_row = node_size_min + np.abs(node_size_max - node_size_min) * weights_row / np.max(weights)
+        node_sizes_col = node_size_min + np.abs(node_size_max - node_size_min) * weights_col / np.max(weights)
+    else:
+        node_sizes_row = node_size * np.ones_like(weights_row)
+        node_sizes_col = node_size * np.ones_like(weights_col)
+    return node_sizes_row, node_sizes_col
+
+
+def get_edge_colors(adjacency: sparse.csr_matrix, edge_labels: Optional[list], edge_color: str,
+                    label_colors: Optional[Iterable]) -> Tuple[np.ndarray, np.ndarray, list]:
+    """Return the edge colors."""
+    n_row, n_col = adjacency.shape
+    n_edges = adjacency.nnz
+    adjacency_labels = (adjacency > 0).astype(int)
+    adjacency_labels.data = -adjacency_labels.data
+    edge_colors_residual = []
+    if edge_labels:
+        label_colors = get_label_colors(label_colors)
+        for i, j, label in edge_labels:
+            if i < 0 or i >= n_row or j < 0 or j >= n_col:
+                raise ValueError('Invalid node index in edge labels.')
+            if adjacency[i, j]:
+                adjacency_labels[i, j] = label % len(label_colors)
+            else:
+                color = label_colors[label % len(label_colors)]
+                edge_colors_residual.append((i, j, color))
+    edge_order = np.argsort(adjacency_labels.data)
+    edge_colors = np.array(n_edges * [edge_color]).astype('U64')
+    index = np.argwhere(adjacency_labels.data >= 0).ravel()
+    if len(index):
+        edge_colors[index] = label_colors[adjacency_labels.data[index]]
+    return edge_colors, edge_order, edge_colors_residual
+
+
+def get_edge_widths(adjacency: sparse.coo_matrix, edge_width: float, edge_width_min: float, edge_width_max: float,
+                    display_edge_weight: bool) -> np.ndarray:
+    """Return the edge widths."""
+    weights = adjacency.data
+    edge_widths = None
+    if len(weights):
+        if display_edge_weight and np.min(weights) < np.max(weights):
+            edge_widths = edge_width_min + np.abs(edge_width_max - edge_width_min) * (weights - np.min(weights))\
+                          / (np.max(weights) - np.min(weights))
+        else:
+            edge_widths = edge_width * np.ones_like(weights)
+    return edge_widths
+
+
+def svg_node(pos_node: np.ndarray, size: float, color: str, stroke_width: float = 1, stroke_color: str = 'black') \
+        -> str:
+    """Return svg code for a node.
+
+    Parameters
+    ----------
+    pos_node :
+        (x, y) coordinates of the node.
+    size :
+        Radius of disk in pixels.
+    color :
+        Color of the disk in SVG valid format.
+    stroke_width :
+        Width of the contour of the disk in pixels, centered around the circle.
+    stroke_color :
+        Color of the contour in SVG valid format.
+
+    Returns
+    -------
+    SVG code for the node.
+    """
+    x, y = pos_node.astype(int)
+    return """<circle cx="{}" cy="{}" r="{}" style="fill:{};stroke:{};stroke-width:{}"/>\n"""\
+        .format(x, y, size, color, stroke_color, stroke_width)
+
+
+def svg_pie_chart_node(pos_node: np.ndarray, size: float, probs: np.ndarray, colors: np.ndarray,
+                       stroke_width: float = 1, stroke_color: str = 'black') -> str:
+    """Return svg code for a pie-chart node."""
+    x, y = pos_node.astype(float)
+    n_colors = len(colors)
+    out = ""
+    cumsum = np.zeros(probs.shape[1] + 1)
+    cumsum[1:] = np.cumsum(probs)
+    if cumsum[-1] == 0:
+        return svg_node(pos_node, size, 'white', stroke_width=3)
+    sum_probs = cumsum[-1]
+    cumsum = np.multiply(cumsum, (2 * np.pi) / cumsum[-1])
+    x_array = size * np.cos(cumsum) + x
+    y_array = size * np.sin(cumsum) + y
+    large = np.array(probs > sum_probs / 2).ravel()
+    for index in range(probs.shape[1]):
+        out += """<path d="M {} {} A {} {} 0 {} 1 {} {} L {} {}" style="fill:{};stroke:{};stroke-width:{}" />\n"""\
+            .format(x_array[index], y_array[index], size, size, int(large[index]),
+                    x_array[index + 1], y_array[index + 1], x, y, colors[index % n_colors], stroke_color, stroke_width)
+    return out
+
+
+def svg_edge(pos_1: np.ndarray, pos_2: np.ndarray, edge_width: float = 1, edge_color: str = 'black') -> str:
+    """Return svg code for an edge."""
+    x1, y1 = pos_1.astype(int)
+    x2, y2 = pos_2.astype(int)
+    return """<path stroke-width="{}" stroke="{}" d="M {} {} {} {}"/>\n"""\
+        .format(edge_width, edge_color, x1, y1, x2, y2)
+
+
+def svg_edge_directed(pos_1: np.ndarray, pos_2: np.ndarray, edge_width: float = 1, edge_color: str = 'black',
+                      node_size: float = 1.) -> str:
+    """Return svg code for a directed edge."""
+    vec = pos_2 - pos_1
+    norm = np.linalg.norm(vec)
+    if norm:
+        x, y = ((vec / norm) * node_size).astype(int)
+        x1, y1 = pos_1.astype(int)
+        x2, y2 = pos_2.astype(int)
+        return """<path stroke-width="{}" stroke="{}" d="M {} {} {} {}" marker-end="url(#arrow-{})"/>\n"""\
+            .format(edge_width, edge_color, x1, y1, x2 - x, y2 - y, edge_color)
+    else:
+        return ""
+
+
+def svg_text(pos, text, margin_text, font_size=12, position: str = 'right'):
+    """Return svg code for text."""
+    if position == 'left':
+        pos[0] -= margin_text
+        anchor = 'end'
+    elif position == 'above':
+        pos[1] -= margin_text
+        anchor = 'middle'
+    elif position == 'below':
+        pos[1] += 2 * margin_text
+        anchor = 'middle'
+    else:
+        pos[0] += margin_text
+        anchor = 'start'
+    x, y = pos.astype(int)
+    text = str(text)
+    for c in ['&', '<', '>']:
+        text = text.replace(c, ' ')
+    return """<text text-anchor="{}" x="{}" y="{}" font-size="{}">{}</text>""".format(anchor, x, y, font_size, text)
+
+
+def visualize_graph(adjacency: Optional[sparse.csr_matrix] = None, position: Optional[np.ndarray] = None,
+                    names: Optional[np.ndarray] = None, labels: Optional[Iterable] = None,
+                    name_position: str = 'right', scores: Optional[Iterable] = None,
+                    probs: Optional[Union[np.ndarray, sparse.csr_matrix]] = None,
+                    seeds: Union[list, dict] = None, width: Optional[float] = 400, height: Optional[float] = 300,
+                    margin: float = 20, margin_text: float = 3, scale: float = 1,
+                    node_order: Optional[np.ndarray] = None, node_size: float = 7, node_size_min: float = 1,
+                    node_size_max: float = 20,
+                    display_node_weight: Optional[bool] = None, node_weights: Optional[np.ndarray] = None,
+                    node_width: float = 1, node_width_max: float = 3, node_color: str = 'gray',
+                    display_edges: bool = True, edge_labels: Optional[list] = None,
+                    edge_width: float = 1, edge_width_min: float = 0.5,
+                    edge_width_max: float = 20, display_edge_weight: bool = False,
+                    edge_color: Optional[str] = None, label_colors: Optional[Iterable] = None,
+                    font_size: int = 12, directed: Optional[bool] = None, filename: Optional[str] = None) -> str:
+    """Return the image of a graph in SVG format.
+
+    Parameters
+    ----------
+    adjacency :
+        Adjacency matrix of the graph.
+    position :
+        Positions of the nodes.
+    names :
+        Names of the nodes.
+    labels :
+        Labels of the nodes (negative values mean no label).
+    name_position :
+        Position of the names (left, right, above, below)
+    scores :
+        Scores of the nodes (measure of importance).
+    probs :
+        Probability distribution over labels.
+    seeds :
+        Nodes to be highlighted (if dict, only keys are considered).
+    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_order :
+        Order in which nodes are displayed.
+    node_size :
+        Size of nodes.
+    node_size_min :
+        Minimum size of a node.
+    node_size_max:
+        Maximum size of a node.
+    node_width :
+        Width of node circle.
+    node_width_max :
+        Maximum width of node circle.
+    node_color :
+        Default color of nodes (svg color).
+    display_node_weight :
+        If ``True``, display node weights through node size.
+    node_weights :
+        Node weights.
+    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).
+    label_colors:
+        Colors of the labels (svg colors).
+    font_size :
+        Font size.
+    directed :
+        If ``True``, considers the graph as directed.
+    filename :
+        Filename for saving image (optional).
+
+    Returns
+    -------
+    image : str
+        SVG image.
+
+    Example
+    -------
+    >>> from sknetwork.data import karate_club
+    >>> graph = karate_club(True)
+    >>> adjacency = graph.adjacency
+    >>> position = graph.position
+    >>> from sknetwork.visualization import visualize_graph
+    >>> image = visualize_graph(adjacency, position)
+    >>> image[1:4]
+    'svg'
+    """
+    # check adjacency
+    if adjacency is None:
+        if position is None:
+            raise ValueError("You must specify either adjacency or position.")
+        else:
+            n = position.shape[0]
+            adjacency = sparse.csr_matrix((n, n)).astype(int)
+    else:
+        n = adjacency.shape[0]
+    adjacency.eliminate_zeros()
+    if directed is None:
+        directed = not is_symmetric(adjacency)
+
+    # node order
+    if node_order is None:
+        node_order = np.arange(n)
+
+    # position
+    if position is None:
+        spring = Spring()
+        position = spring.fit_transform(adjacency)
+
+    # node colors
+    node_colors = get_node_colors(n, labels, scores, probs, node_color, label_colors)
+
+    # node sizes
+    if display_node_weight is None:
+        display_node_weight = node_weights is not None
+    if node_weights is None:
+        node_weights = adjacency.T.dot(np.ones(n))
+    node_sizes = get_node_sizes(node_weights, node_size, node_size_min, node_size_max, display_node_weight)
+
+    # node widths
+    node_widths = get_node_widths(n, seeds, node_width, node_width_max)
+
+    # rescaling
+    position, width, height = rescale(position, width, height, margin, node_size, node_size_max, display_node_weight,
+                                      names, name_position, font_size)
+
+    # scaling
+    position *= scale
+    height *= scale
+    width *= scale
+
+    svg = """<svg width="{}" height="{}" xmlns="http://www.w3.org/2000/svg">\n""".format(width, height)
+
+    # edges
+    if display_edges:
+        adjacency_coo = sparse.coo_matrix(adjacency)
+
+        if edge_color is None:
+            if names is None:
+                edge_color = 'black'
+            else:
+                edge_color = 'gray'
+
+        edge_colors, edge_order, edge_colors_residual = get_edge_colors(adjacency, edge_labels, edge_color,
+                                                                        label_colors)
+        edge_widths = get_edge_widths(adjacency_coo, edge_width, edge_width_min, edge_width_max, display_edge_weight)
+
+        if directed:
+            for edge_color in set(edge_colors):
+                svg += """<defs><marker id="arrow-{}" markerWidth="10" markerHeight="10" refX="9" refY="3"
+                orient="auto" >\n""".format(edge_color)
+                svg += """<path d="M0,0 L0,6 L9,3 z" fill="{}"/></marker></defs>\n""".format(edge_color)
+
+        for ix in edge_order:
+            i = adjacency_coo.row[ix]
+            j = adjacency_coo.col[ix]
+            color = edge_colors[ix]
+            if directed:
+                svg += svg_edge_directed(pos_1=position[i], pos_2=position[j], edge_width=edge_widths[ix],
+                                         edge_color=color, node_size=node_sizes[j])
+            else:
+                svg += svg_edge(pos_1=position[i], pos_2=position[j],
+                                edge_width=edge_widths[ix], edge_color=color)
+
+        for i, j, color in edge_colors_residual:
+            if directed:
+                svg += svg_edge_directed(pos_1=position[i], pos_2=position[j], edge_width=edge_width,
+                                         edge_color=color, node_size=node_sizes[j])
+            else:
+                svg += svg_edge(pos_1=position[i], pos_2=position[j],
+                                edge_width=edge_width, edge_color=color)
+
+    # nodes
+    for i in node_order:
+        if probs is None:
+            svg += svg_node(position[i], node_sizes[i], node_colors[i], node_widths[i])
+        else:
+            probs = check_format(probs)
+            if probs[i].nnz == 1:
+                index = probs[i].indices[0]
+                svg += svg_node(position[i], node_sizes[i], node_colors[index], node_widths[i])
+            else:
+                svg += svg_pie_chart_node(position[i], node_sizes[i], probs[i].todense(),
+                                          node_colors, node_widths[i])
+
+    # text
+    if names is not None:
+        for i in range(n):
+            svg += svg_text(position[i], names[i], node_sizes[i] + margin_text, font_size, name_position)
+    svg += """</svg>\n"""
+
+    if filename is not None:
+        with open(filename + '.svg', 'w') as f:
+            f.write(svg)
+
+    return svg
+
+
+def visualize_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,
+                      probs_row: Optional[Union[np.ndarray, sparse.csr_matrix]] = None,
+                      probs_col: Optional[Union[np.ndarray, 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 the image of a bipartite graph in SVG format.
+
+    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).
+    probs_row :
+        Probability distribution over labels for rows.
+    probs_col :
+        Probability distribution over labels for columns.
+    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 visualize_bigraph
+    >>> image = visualize_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:
+            louvain = Louvain()
+            louvain.fit(biadjacency, force_bipartite=True)
+            index_row = np.argsort(louvain.labels_row_)
+            index_col = np.argsort(louvain.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
+    if scores_row is not None and scores_col is not None:
+        if isinstance(scores_row, dict):
+            scores_row = np.array(list(scores_row.values()))
+        if isinstance(scores_col, dict):
+            scores_col = np.array(list(scores_col.values()))
+        scores = np.hstack((scores_row, scores_col))
+        score_min = np.min(scores)
+        score_max = np.max(scores)
+    else:
+        score_min = None
+        score_max = None
+
+    colors_row = get_node_colors(n_row, labels_row, scores_row, probs_row, color_row, label_colors,
+                                 score_min, score_max)
+    colors_col = get_node_colors(n_col, labels_col, scores_col, probs_col, color_col, label_colors,
+                                 score_min, score_max)
+
+    # 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 probs_row is None:
+            svg += svg_node(position_row[i], node_sizes_row[i], colors_row[i], node_widths_row[i])
+        else:
+            probs_row = check_format(probs_row)
+            if probs_row[i].nnz == 1:
+                index = probs_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], probs_row[i].todense(),
+                                          colors_row, node_widths_row[i])
+
+    for i in range(n_col):
+        if probs_col is None:
+            svg += svg_node(position_col[i], node_sizes_col[i], colors_col[i], node_widths_col[i])
+        else:
+            probs_col = check_format(probs_col)
+            if probs_col[i].nnz == 1:
+                index = probs_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], probs_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], names_row[i], margin_text + node_sizes_row[i], font_size, 'left')
+    if names_col is not None:
+        for i in range(n_col):
+            svg += svg_text(position_col[i], names_col[i], margin_text + node_sizes_col[i], font_size)
+    svg += """</svg>\n"""
+
+    if filename is not None:
+        with open(filename + '.svg', 'w') as f:
+            f.write(svg)
+
+    return svg
+
+
+def svg_graph(adjacency: Optional[sparse.csr_matrix] = None, position: Optional[np.ndarray] = None,
+              names: Optional[np.ndarray] = None, labels: Optional[Iterable] = None, name_position: str = 'right',
+              scores: Optional[Iterable] = None, probs: Optional[Union[np.ndarray, sparse.csr_matrix]] = None,
+              seeds: Union[list, dict] = None, width: Optional[float] = 400, height: Optional[float] = 300,
+              margin: float = 20, margin_text: float = 3, scale: float = 1, node_order: Optional[np.ndarray] = None,
+              node_size: float = 7, node_size_min: float = 1, node_size_max: float = 20,
+              display_node_weight: Optional[bool] = None, node_weights: Optional[np.ndarray] = None,
+              node_width: float = 1, node_width_max: float = 3, node_color: str = 'gray',
+              display_edges: bool = True, edge_labels: Optional[list] = None,
+              edge_width: float = 1, edge_width_min: float = 0.5,
+              edge_width_max: float = 20, display_edge_weight: bool = True,
+              edge_color: Optional[str] = None, label_colors: Optional[Iterable] = None,
+              font_size: int = 12, directed: Optional[bool] = None, filename: Optional[str] = None) -> str:
+    """Return the image of a graph in SVG format.
+
+    Alias for visualize_graph.
+
+    Parameters
+    ----------
+    adjacency :
+        Adjacency matrix of the graph.
+    position :
+        Positions of the nodes.
+    names :
+        Names of the nodes.
+    labels :
+        Labels of the nodes (negative values mean no label).
+    name_position :
+        Position of the names (left, right, above, below)
+    scores :
+        Scores of the nodes (measure of importance).
+    probs :
+        Probability distribution over labels.
+    seeds :
+        Nodes to be highlighted (if dict, only keys are considered).
+    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_order :
+        Order in which nodes are displayed.
+    node_size :
+        Size of nodes.
+    node_size_min :
+        Minimum size of a node.
+    node_size_max:
+        Maximum size of a node.
+    node_width :
+        Width of node circle.
+    node_width_max :
+        Maximum width of node circle.
+    node_color :
+        Default color of nodes (svg color).
+    display_node_weight :
+        If ``True``, display node weights through node size.
+    node_weights :
+        Node weights.
+    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).
+    label_colors:
+        Colors of the labels (svg colors).
+    font_size :
+        Font size.
+    directed :
+        If ``True``, considers the graph as directed.
+    filename :
+        Filename for saving image (optional).
+
+    Returns
+    -------
+    image : str
+        SVG image.
+    """
+    return visualize_graph(adjacency, position, names, labels, name_position, scores, probs, seeds, width, height,
+                           margin, margin_text, scale, node_order, node_size, node_size_min, node_size_max,
+                           display_node_weight, node_weights, node_width, node_width_max, node_color, display_edges,
+                           edge_labels, edge_width, edge_width_min, edge_width_max, display_edge_weight, edge_color,
+                           label_colors, font_size, directed, filename)
+
+
+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,
+                probs_row: Optional[Union[np.ndarray, sparse.csr_matrix]] = None,
+                probs_col: Optional[Union[np.ndarray, 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 the image of a bipartite graph in SVG format.
+
+    Alias for visualize_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).
+    probs_row :
+        Probability distribution over labels for rows.
+    probs_col :
+        Probability distribution over labels for columns.
+    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.
+    """
+    return visualize_bigraph(biadjacency, names_row, names_col, labels_row, labels_col, scores_row, scores_col,
+                             probs_row, probs_col, seeds_row, seeds_col, position_row, position_col, reorder,
+                             width, height, margin, margin_text, scale, node_size, node_size_min, node_size_max,
+                             display_node_weight, node_weights_row, node_weights_col, node_width, node_width_max,
+                             color_row, color_col, label_colors, display_edges, edge_labels, edge_width, edge_width_min,
+                             edge_width_max, edge_color, display_edge_weight, font_size, filename)