#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created in April 2020
@author: Thomas Bonald <bonald@enst.fr>
"""
from typing import Iterable, Optional
import numpy as np
from sknetwork.hierarchy.postprocess import cut_straight
from sknetwork.visualization.colors import STANDARD_COLORS
def get_index(dendrogram, reorder=True):
"""Index nodes for pretty dendrogram."""
n = dendrogram.shape[0] + 1
tree = {i: [i] for i in range(n)}
for t in range(n - 1):
i = int(dendrogram[t, 0])
j = int(dendrogram[t, 1])
left: list = tree.pop(i)
right: list = tree.pop(j)
if reorder and len(left) < len(right):
tree[n + t] = right + left
else:
tree[n + t] = left + right
return list(tree.values())[0]
def svg_dendrogram_top(dendrogram, names, width, height, margin, margin_text, scale, line_width, n_clusters,
color, colors, font_size, reorder, rotate_names):
"""Dendrogram as SVG image with root on top."""
# scaling
height *= scale
width *= scale
# positioning
labels = cut_straight(dendrogram, n_clusters, return_dendrogram=False)
index = get_index(dendrogram, reorder)
n = len(index)
unit_height = height / dendrogram[-1, 2]
unit_width = width / n
height_basis = margin + height
position = {index[i]: (margin + i * unit_width, height_basis) for i in range(n)}
label = {i: l for i, l in enumerate(labels)}
width += 2 * margin
height += 2 * margin
if names is not None:
text_length = np.max(np.array([len(str(name)) for name in names]))
height += text_length * font_size * .5 + margin_text
svg = """<svg width="{}" height="{}" xmlns="http://www.w3.org/2000/svg">""".format(width, height)
# text
if names is not None:
for i in range(n):
x, y = position[i]
x -= margin_text
y += margin_text
text = str(names[i]).replace('&', ' ')
if rotate_names:
svg += """<text x="{}" y="{}" transform="rotate(60, {}, {})" font-size="{}">{}</text>""" \
.format(x, y, x, y, font_size, text)
else:
y += margin_text
svg += """<text x="{}" y="{}" font-size="{}">{}</text>""" \
.format(x, y, font_size, text)
# tree
for t in range(n - 1):
i = int(dendrogram[t, 0])
j = int(dendrogram[t, 1])
x1, y1 = position.pop(i)
x2, y2 = position.pop(j)
l1 = label.pop(i)
l2 = label.pop(j)
if l1 == l2:
line_color = colors[l1 % len(colors)]
else:
line_color = color
x = .5 * (x1 + x2)
y = height_basis - dendrogram[t, 2] * unit_height
svg += """<path stroke-width="{}" stroke="{}" d="M {} {} {} {}" />"""\
.format(line_width, line_color, x1, y1, x1, y)
svg += """<path stroke-width="{}" stroke="{}" d="M {} {} {} {}" />"""\
.format(line_width, line_color, x2, y2, x2, y)
svg += """<path stroke-width="{}" stroke="{}" d="M {} {} {} {}" />"""\
.format(line_width, line_color, x1, y, x2, y)
position[n + t] = (x, y)
label[n + t] = l1
svg += '</svg>'
return svg
def svg_dendrogram_left(dendrogram, names, width, height, margin, margin_text, scale, line_width, n_clusters,
color, colors, font_size, reorder):
"""Dendrogram as SVG image with root on left side."""
# scaling
height *= scale
width *= scale
# positioning
labels = cut_straight(dendrogram, n_clusters, return_dendrogram=False)
index = get_index(dendrogram, reorder)
n = len(index)
unit_height = height / n
unit_width = width / dendrogram[-1, 2]
width_basis = width + margin
position = {index[i]: (width_basis, margin + i * unit_height) for i in range(n)}
label = {i: l for i, l in enumerate(labels)}
width += 2 * margin
height += 2 * margin
if names is not None:
text_length = np.max(np.array([len(str(name)) for name in names]))
width += text_length * font_size * .5 + margin_text
svg = """<svg width="{}" height="{}" xmlns="http://www.w3.org/2000/svg">""".format(width, height)
# text
if names is not None:
for i in range(n):
x, y = position[i]
x += margin_text
y += unit_height / 3
text = str(names[i]).replace('&', ' ')
svg += """<text x="{}" y="{}" font-size="{}">{}</text>""" \
.format(x, y, font_size, text)
# tree
for t in range(n - 1):
i = int(dendrogram[t, 0])
j = int(dendrogram[t, 1])
x1, y1 = position.pop(i)
x2, y2 = position.pop(j)
l1 = label.pop(i)
l2 = label.pop(j)
if l1 == l2:
line_color = colors[l1 % len(colors)]
else:
line_color = color
y = .5 * (y1 + y2)
x = width_basis - dendrogram[t, 2] * unit_width
svg += """<path stroke-width="{}" stroke="{}" d="M {} {} {} {}" />"""\
.format(line_width, line_color, x1, y1, x, y1)
svg += """<path stroke-width="{}" stroke="{}" d="M {} {} {} {}" />"""\
.format(line_width, line_color, x2, y2, x, y2)
svg += """<path stroke-width="{}" stroke="{}" d="M {} {} {} {}" />"""\
.format(line_width, line_color, x, y1, x, y2)
position[n + t] = (x, y)
label[n + t] = l1
svg += '</svg>'
return svg
[docs]def visualize_dendrogram(dendrogram: np.ndarray, names: Optional[np.ndarray] = None, rotate: bool = False,
width: float = 400, height: float = 300, margin: float = 10, margin_text: float = 5,
scale: float = 1, line_width: float = 2, n_clusters: int = 2, color: str = 'black',
colors: Optional[Iterable] = None, font_size: int = 12, reorder: bool = False,
rotate_names: bool = True, filename: Optional[str] = None):
"""Return the image of a dendrogram in SVG format.
Parameters
----------
dendrogram :
Dendrogram to display.
names :
Names of leaves.
rotate :
If ``True``, rotate the tree so that the root is on the left.
width :
Width of the image (margins excluded).
height :
Height of the image (margins excluded).
margin :
Margin.
margin_text :
Margin between leaves and their names, if any.
scale :
Scaling factor.
line_width :
Line width.
n_clusters :
Number of coloured clusters to display.
color :
Default SVG color for the dendrogram.
colors :
SVG colors of the clusters of the dendrogram (optional).
font_size :
Font size.
reorder :
If ``True``, reorder leaves so that left subtree has more leaves than right subtree.
rotate_names :
If ``True``, rotate names of leaves (only valid if **rotate** is ``False``).
filename :
Filename for saving image (optional).
Example
-------
>>> dendrogram = np.array([[0, 1, 1, 2], [2, 3, 2, 3]])
>>> from sknetwork.visualization import svg_dendrogram
>>> image = svg_dendrogram(dendrogram)
>>> image[1:4]
'svg'
"""
if colors is None:
colors = STANDARD_COLORS
elif isinstance(colors, dict):
colors = np.array(list(colors.values()))
elif isinstance(colors, list):
colors = np.array(colors)
if rotate:
svg = svg_dendrogram_left(dendrogram, names, width, height, margin, margin_text, scale, line_width, n_clusters,
color, colors, font_size, reorder)
else:
svg = svg_dendrogram_top(dendrogram, names, width, height, margin, margin_text, scale, line_width, n_clusters,
color, colors, font_size, reorder, rotate_names)
if filename is not None:
with open(filename + '.svg', 'w') as f:
f.write(svg)
return svg
def svg_dendrogram(dendrogram: np.ndarray, names: Optional[np.ndarray] = None, rotate: bool = False, width: float = 400,
height: float = 300, margin: float = 10, margin_text: float = 5, scale: float = 1,
line_width: float = 2, n_clusters: int = 2, color: str = 'black', colors: Optional[Iterable] = None,
font_size: int = 12, reorder: bool = False, rotate_names: bool = True,
filename: Optional[str] = None):
"""Return the image of a dendrogram in SVG format.
Alias for visualize_dendrogram.
Parameters
----------
dendrogram :
Dendrogram to display.
names :
Names of leaves.
rotate :
If ``True``, rotate the tree so that the root is on the left.
width :
Width of the image (margins excluded).
height :
Height of the image (margins excluded).
margin :
Margin.
margin_text :
Margin between leaves and their names, if any.
scale :
Scaling factor.
line_width :
Line width.
n_clusters :
Number of coloured clusters to display.
color :
Default SVG color for the dendrogram.
colors :
SVG colors of the clusters of the dendrogram (optional).
font_size :
Font size.
reorder :
If ``True``, reorder leaves so that left subtree has more leaves than right subtree.
rotate_names :
If ``True``, rotate names of leaves (only valid if **rotate** is ``False``).
filename :
Filename for saving image (optional).
"""
return visualize_dendrogram(dendrogram, names, rotate, width, height, margin, margin_text, scale, line_width,
n_clusters, color, colors, font_size, reorder, rotate_names, filename)