# -*- coding: utf-8 -*-
#
# This file is part of Sequana software
#
# Copyright (c) 2016 - Sequana Development Team
#
# File author(s):
# Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
# Etienne Kornobis <etienne.kornobis@pasteur.fr>,
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with this software.
#
# website: https://github.com/sequana/sequana
# documentation: http://sequana.readthedocs.io
#
##############################################################################
from sequana.lazy import pylab
__all__ = ["plot_venn", "default_colors", "get_layout"]
import math
from itertools import chain
from sequana.lazy import pylab
default_colors = [
[92 / 255.0, 192 / 255.0, 98 / 255.0, 0.5],
[90 / 255.0, 155 / 255.0, 212 / 255.0, 0.5],
[246 / 255.0, 236 / 255.0, 86 / 255.0, 0.6],
[241 / 255.0, 90 / 255.0, 96 / 255.0, 0.4],
[255 / 255.0, 117 / 255.0, 0 / 255.0, 0.3],
[82 / 255.0, 82 / 255.0, 190 / 255.0, 0.2],
]
[docs]
def get_layout(num_sets):
"""Get Venn diagram layout for n sets.
Returns a dict with shapes and text positions for the given number of sets.
Supports 2 to 6 sets.
"""
if num_sets == 2:
return {
"shapes": [
("ellipse", {"xy": (0.375, 0.5), "width": 0.6, "height": 0.6, "angle": 0}),
("ellipse", {"xy": (0.625, 0.5), "width": 0.6, "height": 0.6, "angle": 0}),
],
"texts": [
{"x": 0.26, "y": 0.50, "text": "", "fontsize": 12},
{"x": 0.50, "y": 0.50, "text": "", "fontsize": 12},
{"x": 0.74, "y": 0.50, "text": "", "fontsize": 12},
],
"names": [
{"x": 0.25, "y": 0.15},
{"x": 0.75, "y": 0.15},
],
}
elif num_sets == 3:
return {
"shapes": [
("ellipse", {"xy": (0.33, 0.5), "width": 0.5, "height": 0.7, "angle": 0}),
("ellipse", {"xy": (0.67, 0.5), "width": 0.5, "height": 0.7, "angle": 0}),
("ellipse", {"xy": (0.50, 0.25), "width": 0.5, "height": 0.7, "angle": 0}),
],
"texts": [
{"x": 0.20, "y": 0.60, "text": "", "fontsize": 10},
{"x": 0.80, "y": 0.60, "text": "", "fontsize": 10},
{"x": 0.50, "y": 0.05, "text": "", "fontsize": 10},
{"x": 0.50, "y": 0.50, "text": "", "fontsize": 10},
{"x": 0.35, "y": 0.30, "text": "", "fontsize": 10},
{"x": 0.65, "y": 0.30, "text": "", "fontsize": 10},
{"x": 0.50, "y": 0.20, "text": "", "fontsize": 10},
],
"names": [
{"x": 0.15, "y": 0.85},
{"x": 0.85, "y": 0.85},
{"x": 0.50, "y": 0.05},
],
}
elif num_sets == 4:
# Four rotated ellipses arranged symmetrically
return {
"shapes": [
("ellipse", {"xy": (0.37, 0.58), "width": 0.45, "height": 0.80, "angle": -30}),
("ellipse", {"xy": (0.63, 0.58), "width": 0.45, "height": 0.80, "angle": 30}),
("ellipse", {"xy": (0.37, 0.42), "width": 0.45, "height": 0.80, "angle": 30}),
("ellipse", {"xy": (0.63, 0.42), "width": 0.45, "height": 0.80, "angle": -30}),
],
"texts": [],
"names": [
{"x": 0.10, "y": 0.85, "ha": "left", "va": "top"},
{"x": 0.90, "y": 0.85, "ha": "right", "va": "top"},
{"x": 0.10, "y": 0.15, "ha": "left", "va": "bottom"},
{"x": 0.90, "y": 0.15, "ha": "right", "va": "bottom"},
],
}
elif num_sets == 5:
# Five ellipses at 72-degree intervals around the centre
import math
shapes = []
names = []
for i in range(5):
angle_deg = 90 - i * 72
angle_rad = math.radians(angle_deg)
cx = 0.5 + 0.17 * math.cos(angle_rad)
cy = 0.5 + 0.17 * math.sin(angle_rad)
shapes.append(
(
"ellipse",
{"xy": (round(cx, 3), round(cy, 3)), "width": 0.45, "height": 0.75, "angle": angle_deg - 90},
)
)
nx = 0.5 + 0.52 * math.cos(angle_rad)
ny = 0.5 + 0.52 * math.sin(angle_rad)
names.append({"x": round(nx, 3), "y": round(ny, 3), "ha": "center", "va": "center"})
return {"shapes": shapes, "texts": [], "names": names}
elif num_sets == 6:
# Six ellipses at 60-degree intervals around the centre
import math
shapes = []
names = []
for i in range(6):
angle_deg = 90 - i * 60
angle_rad = math.radians(angle_deg)
cx = 0.5 + 0.15 * math.cos(angle_rad)
cy = 0.5 + 0.15 * math.sin(angle_rad)
shapes.append(
(
"ellipse",
{"xy": (round(cx, 3), round(cy, 3)), "width": 0.40, "height": 0.75, "angle": angle_deg - 90},
)
)
nx = 0.5 + 0.50 * math.cos(angle_rad)
ny = 0.5 + 0.50 * math.sin(angle_rad)
names.append({"x": round(nx, 3), "y": round(ny, 3), "ha": "center", "va": "center"})
return {"shapes": shapes, "texts": [], "names": names}
else:
return {"shapes": [], "texts": [], "names": []}
def draw_shape(ax, shape, params, fillcolor):
"""
General function to draw a shape (ellipse, polygon).
"""
import matplotlib.patches as patches
if shape == "ellipse":
shape_obj = patches.Ellipse(**params, color=fillcolor, lw=3)
elif shape == "polygon":
shape_obj = patches.Polygon(params["xy"], closed=True, color=fillcolor)
else:
raise ValueError(f"Unsupported shape: {shape}")
ax.add_patch(shape_obj)
def draw_text(ax, x, y, text, color="black", fontsize=14, ha="center", va="center"):
"""
Draw text on the plot.
"""
ax.text(x, y, text, fontsize=fontsize, color=color, ha=ha, va=va)
def get_labels(data, fill=["number"]):
"""
Generate a dictionary of labels for the Venn diagram.
"""
N = len(data)
sets_data = [set(d) for d in data]
union_all = set(chain(*data))
set_collections = {}
for n in range(1, 2**N):
key = bin(n)[2:].zfill(N)
included = [sets_data[i] for i, b in enumerate(key) if b == "1"]
excluded = [sets_data[i] for i, b in enumerate(key) if b == "0"]
intersection = set.intersection(*included) if included else union_all
difference = intersection - set.union(*excluded) if excluded else intersection
set_collections[key] = difference
labels = {k: "" for k in set_collections}
for k, values in set_collections.items():
if "logic" in fill:
labels[k] += f"{k}: "
if "number" in fill:
labels[k] += str(len(values))
if "percent" in fill:
labels[k] += f" ({100 * len(values) / len(union_all):.1f}%)"
return labels
def _venn_plot(labels, names, layout, colors=None, figsize=(9, 9), dpi=96, fontsize=14):
"""
General function to create a Venn diagram with configurable layout.
"""
colors = colors or [default_colors[i] for i in range(len(layout["shapes"]))]
fig, ax = pylab.subplots(figsize=figsize, dpi=dpi)
ax.set_axis_off()
ax.set_xlim(0, 1)
ax.set_ylim(0, 1)
# Draw shapes and labels
for i, (shape, params) in enumerate(layout["shapes"]):
draw_shape(ax, shape, params, colors[i])
for text_params in layout["texts"]:
draw_text(ax, **text_params)
# Add group names
for i, name in enumerate(names):
draw_text(ax, **layout["names"][i], text=name, color="k")
leg = ax.legend(names, loc="center left", bbox_to_anchor=(1.0, 0.5), fancybox=True)
leg.get_frame().set_alpha(0.5)
return fig, ax
def venn2(labels, names=["A", "B"], **options):
"""
Plot a 2-set Venn diagram.
"""
layout = {
"shapes": [
("ellipse", {"xy": (0.375, 0.5), "width": 0.6, "height": 0.6, "angle": 0}),
("ellipse", {"xy": (0.625, 0.5), "width": 0.6, "height": 0.6, "angle": 0}),
],
"texts": [
{"x": 0.74, "y": 0.50, "text": labels.get("01", "")},
{"x": 0.26, "y": 0.50, "text": labels.get("10", "")},
{"x": 0.50, "y": 0.50, "text": labels.get("11", "")},
],
"names": [
{"x": 0.20, "y": 0.76, "ha": "right", "va": "bottom"},
{"x": 0.80, "y": 0.76, "ha": "left", "va": "bottom"},
],
}
return _venn_plot(labels, names, layout, **options)
def venn3(labels, names=["A", "B", "C"], **options):
"""
Plot a 3-set Venn diagram.
"""
layout = {
"shapes": [
("ellipse", {"xy": (0.333, 0.633), "width": 0.5, "height": 0.5, "angle": 0}),
("ellipse", {"xy": (0.666, 0.633), "width": 0.5, "height": 0.5, "angle": 0}),
("ellipse", {"xy": (0.500, 0.310), "width": 0.5, "height": 0.5, "angle": 0}),
],
"texts": [
{"x": 0.50, "y": 0.27, "text": labels.get("001", "")},
{"x": 0.73, "y": 0.65, "text": labels.get("010", "")},
{"x": 0.61, "y": 0.46, "text": labels.get("011", "")},
{"x": 0.27, "y": 0.65, "text": labels.get("100", "")},
{"x": 0.39, "y": 0.46, "text": labels.get("101", "")},
{"x": 0.50, "y": 0.65, "text": labels.get("110", "")},
{"x": 0.50, "y": 0.51, "text": labels.get("111", "")},
],
"names": [
{"x": 0.15, "y": 0.87, "ha": "right", "va": "bottom"},
{"x": 0.85, "y": 0.87, "ha": "left", "va": "bottom"},
{"x": 0.50, "y": 0.02, "ha": "center", "va": "top"},
],
}
return _venn_plot(labels, names, layout, **options)
def venn4(labels, names=["A", "B", "C", "D"], **options):
"""
Plot a 4-set Venn diagram.
"""
layout = {
"shapes": [
("ellipse", {"xy": (0.35, 0.4), "width": 0.72, "height": 0.45, "angle": 140}),
("ellipse", {"xy": (0.45, 0.5), "width": 0.72, "height": 0.45, "angle": 140}),
("ellipse", {"xy": (0.544, 0.5), "width": 0.72, "height": 0.45, "angle": 40}),
("ellipse", {"xy": (0.644, 0.4), "width": 0.72, "height": 0.45, "angle": 40}),
],
"texts": [
{"x": 0.85, "y": 0.42, "text": labels.get("0001", "")},
{"x": 0.68, "y": 0.72, "text": labels.get("0010", "")},
{"x": 0.77, "y": 0.59, "text": labels.get("0011", "")},
{"x": 0.32, "y": 0.72, "text": labels.get("0100", "")},
{"x": 0.71, "y": 0.30, "text": labels.get("0101", "")},
{"x": 0.50, "y": 0.66, "text": labels.get("0110", "")},
{"x": 0.65, "y": 0.50, "text": labels.get("0111", "")},
{"x": 0.14, "y": 0.42, "text": labels.get("1000", "")},
{"x": 0.50, "y": 0.17, "text": labels.get("1001", "")},
{"x": 0.29, "y": 0.30, "text": labels.get("1010", "")},
{"x": 0.39, "y": 0.24, "text": labels.get("1011", "")},
{"x": 0.23, "y": 0.59, "text": labels.get("1100", "")},
{"x": 0.61, "y": 0.24, "text": labels.get("1101", "")},
{"x": 0.35, "y": 0.50, "text": labels.get("1110", "")},
{"x": 0.50, "y": 0.38, "text": labels.get("1111", "")},
],
"names": [
{"x": 0.13, "y": 0.18, "ha": "center", "va": "center"},
{"x": 0.18, "y": 0.83, "ha": "center", "va": "center"},
{"x": 0.82, "y": 0.83, "ha": "center", "va": "center"},
{"x": 0.87, "y": 0.18, "ha": "center", "va": "center"},
],
}
return _venn_plot(labels, names, layout, **options)
def venn5(labels, names=["A", "B", "C", "D", "E"], **options):
"""
Plot a 5-set Venn diagram.
"""
layout = {
"shapes": [
("ellipse", {"xy": (0.428, 0.449), "width": 0.87, "height": 0.5, "angle": 155}),
("ellipse", {"xy": (0.469, 0.543), "width": 0.87, "height": 0.5, "angle": 82}),
("ellipse", {"xy": (0.558, 0.523), "width": 0.87, "height": 0.5, "angle": 10}),
("ellipse", {"xy": (0.578, 0.432), "width": 0.87, "height": 0.5, "angle": 118}),
("ellipse", {"xy": (0.489, 0.383), "width": 0.87, "height": 0.5, "angle": 46}),
],
"texts": [
{"x": 0.27, "y": 0.11, "text": labels.get("00001", "")},
{"x": 0.72, "y": 0.11, "text": labels.get("00010", "")},
{"x": 0.55, "y": 0.13, "text": labels.get("00011", "")},
{"x": 0.91, "y": 0.58, "text": labels.get("00100", "")},
{"x": 0.78, "y": 0.64, "text": labels.get("00101", "")},
{"x": 0.84, "y": 0.41, "text": labels.get("00110", "")},
{"x": 0.76, "y": 0.55, "text": labels.get("00111", "")},
{"x": 0.51, "y": 0.90, "text": labels.get("01000", "")},
{"x": 0.39, "y": 0.15, "text": labels.get("01001", "")},
{"x": 0.42, "y": 0.78, "text": labels.get("01010", "")},
{"x": 0.50, "y": 0.15, "text": labels.get("01011", "")},
{"x": 0.67, "y": 0.76, "text": labels.get("01100", "")},
{"x": 0.70, "y": 0.71, "text": labels.get("01101", "")},
{"x": 0.51, "y": 0.74, "text": labels.get("01110", "")},
{"x": 0.64, "y": 0.67, "text": labels.get("01111", "")},
{"x": 0.10, "y": 0.61, "text": labels.get("10000", "")},
{"x": 0.20, "y": 0.31, "text": labels.get("10001", "")},
{"x": 0.76, "y": 0.25, "text": labels.get("10010", "")},
{"x": 0.65, "y": 0.23, "text": labels.get("10011", "")},
{"x": 0.18, "y": 0.50, "text": labels.get("10100", "")},
{"x": 0.21, "y": 0.37, "text": labels.get("10101", "")},
{"x": 0.81, "y": 0.37, "text": labels.get("10110", "")},
{"x": 0.74, "y": 0.40, "text": labels.get("10111", "")},
{"x": 0.27, "y": 0.70, "text": labels.get("11000", "")},
{"x": 0.34, "y": 0.25, "text": labels.get("11001", "")},
{"x": 0.33, "y": 0.72, "text": labels.get("11010", "")},
{"x": 0.51, "y": 0.22, "text": labels.get("11011", "")},
{"x": 0.25, "y": 0.58, "text": labels.get("11100", "")},
{"x": 0.28, "y": 0.39, "text": labels.get("11101", "")},
{"x": 0.36, "y": 0.66, "text": labels.get("11110", "")},
{"x": 0.51, "y": 0.47, "text": labels.get("11111", "")},
],
"names": [
{"x": 0.0, "y": 0.62, "ha": "center", "va": "center"},
{"x": 0.52, "y": 1.0, "ha": "center", "va": "center"},
{"x": 0.99, "y": 0.74, "ha": "center", "va": "center"},
{"x": 0.78, "y": 0.0, "ha": "center", "va": "center"},
{"x": 0.22, "y": 0.0, "ha": "center", "va": "center"},
],
}
return _venn_plot(labels, names, layout, **options)
def venn6(labels, names=["A", "B", "C", "D"], **options):
"""
Plot a 6-set Venn diagram.
"""
layout = {
"shapes": [
("polygon", {"xy": [(0.637, 0.921), (0.649, 0.274), (0.188, 0.667)]}),
("polygon", {"xy": [(0.981, 0.769), (0.335, 0.191), (0.393, 0.671)]}),
("polygon", {"xy": [(0.941, 0.397), (0.292, 0.475), (0.456, 0.747)]}),
("polygon", {"xy": [(0.662, 0.119), (0.316, 0.548), (0.662, 0.700)]}),
("polygon", {"xy": [(0.309, 0.081), (0.374, 0.718), (0.681, 0.488)]}),
("polygon", {"xy": [(0.016, 0.626), (0.726, 0.687), (0.522, 0.327)]}),
],
"texts": [
{"x": 0.212, "y": 0.562, "text": labels.get("000001", "")},
{"x": 0.430, "y": 0.249, "text": labels.get("000010", "")},
{"x": 0.356, "y": 0.444, "text": labels.get("000011", "")},
{"x": 0.609, "y": 0.255, "text": labels.get("000100", "")},
{"x": 0.323, "y": 0.546, "text": labels.get("000101", "")},
{"x": 0.513, "y": 0.316, "text": labels.get("000110", "")},
{"x": 0.523, "y": 0.348, "text": labels.get("000111", "")},
{"x": 0.747, "y": 0.458, "text": labels.get("001000", "")},
{"x": 0.325, "y": 0.492, "text": labels.get("001001", "")},
{"x": 0.670, "y": 0.481, "text": labels.get("001010", "")},
{"x": 0.359, "y": 0.478, "text": labels.get("001011", "")},
{"x": 0.653, "y": 0.444, "text": labels.get("001100", "")},
{"x": 0.344, "y": 0.526, "text": labels.get("001101", "")},
{"x": 0.653, "y": 0.466, "text": labels.get("001110", "")},
{"x": 0.363, "y": 0.503, "text": labels.get("001111", "")},
{"x": 0.750, "y": 0.616, "text": labels.get("010000", "")},
{"x": 0.682, "y": 0.654, "text": labels.get("010001", "")},
{"x": 0.402, "y": 0.310, "text": labels.get("010010", "")},
{"x": 0.392, "y": 0.421, "text": labels.get("010011", "")},
{"x": 0.653, "y": 0.691, "text": labels.get("010100", "")},
{"x": 0.651, "y": 0.644, "text": labels.get("010101", "")},
{"x": 0.490, "y": 0.340, "text": labels.get("010110", "")},
{"x": 0.468, "y": 0.399, "text": labels.get("010111", "")},
{"x": 0.692, "y": 0.545, "text": labels.get("011000", "")},
{"x": 0.666, "y": 0.592, "text": labels.get("011001", "")},
{"x": 0.665, "y": 0.496, "text": labels.get("011010", "")},
{"x": 0.374, "y": 0.470, "text": labels.get("011011", "")},
{"x": 0.653, "y": 0.537, "text": labels.get("011100", "")},
{"x": 0.652, "y": 0.579, "text": labels.get("011101", "")},
{"x": 0.653, "y": 0.488, "text": labels.get("011110", "")},
{"x": 0.389, "y": 0.486, "text": labels.get("011111", "")},
{"x": 0.553, "y": 0.806, "text": labels.get("100000", "")},
{"x": 0.313, "y": 0.604, "text": labels.get("100001", "")},
{"x": 0.388, "y": 0.694, "text": labels.get("100010", "")},
{"x": 0.375, "y": 0.633, "text": labels.get("100011", "")},
{"x": 0.605, "y": 0.359, "text": labels.get("100100", "")},
{"x": 0.334, "y": 0.555, "text": labels.get("100101", "")},
{"x": 0.582, "y": 0.397, "text": labels.get("100110", "")},
{"x": 0.542, "y": 0.372, "text": labels.get("100111", "")},
{"x": 0.468, "y": 0.708, "text": labels.get("101000", "")},
{"x": 0.355, "y": 0.572, "text": labels.get("101001", "")},
{"x": 0.420, "y": 0.679, "text": labels.get("101010", "")},
{"x": 0.375, "y": 0.597, "text": labels.get("101011", "")},
{"x": 0.641, "y": 0.436, "text": labels.get("101100", "")},
{"x": 0.348, "y": 0.538, "text": labels.get("101101", "")},
{"x": 0.635, "y": 0.453, "text": labels.get("101110", "")},
{"x": 0.370, "y": 0.548, "text": labels.get("101111", "")},
{"x": 0.594, "y": 0.689, "text": labels.get("110000", "")},
{"x": 0.579, "y": 0.670, "text": labels.get("110001", "")},
{"x": 0.398, "y": 0.670, "text": labels.get("110010", "")},
{"x": 0.395, "y": 0.653, "text": labels.get("110011", "")},
{"x": 0.633, "y": 0.682, "text": labels.get("110100", "")},
{"x": 0.616, "y": 0.656, "text": labels.get("110101", "")},
{"x": 0.587, "y": 0.427, "text": labels.get("110110", "")},
{"x": 0.526, "y": 0.415, "text": labels.get("110111", "")},
{"x": 0.495, "y": 0.677, "text": labels.get("111000", "")},
{"x": 0.505, "y": 0.648, "text": labels.get("111001", "")},
{"x": 0.428, "y": 0.663, "text": labels.get("111010", "")},
{"x": 0.430, "y": 0.631, "text": labels.get("111011", "")},
{"x": 0.639, "y": 0.524, "text": labels.get("111100", "")},
{"x": 0.591, "y": 0.604, "text": labels.get("111101", "")},
{"x": 0.622, "y": 0.477, "text": labels.get("111110", "")},
{"x": 0.501, "y": 0.523, "text": labels.get("111111", "")},
],
"names": [
{"x": 0.674, "y": 0.824, "ha": "center", "va": "center"},
{"x": 0.747, "y": 0.751, "ha": "center", "va": "center"},
{"x": 0.739, "y": 0.396, "ha": "center", "va": "center"},
{"x": 0.700, "y": 0.247, "ha": "center", "va": "center"},
{"x": 0.291, "y": 0.255, "ha": "center", "va": "center"},
{"x": 0.203, "y": 0.484, "ha": "center", "va": "center"},
],
}
return _venn_plot(labels, names, layout, **options)
[docs]
def plot_venn(subsets, labels=None, title=None, ax=None, alpha=0.8, weighted=False, colors=("r", "b", "y")):
"""Plot venn diagramm according to number of groups.
:param subsets: This parameter may be (1) a dict, providing sizes of
three diagram regions. The regions are identified via two-letter
binary codes ('10', '01', and '11'), hence a valid set could look like:
{'10': 10, '01': 20, '11': 40}. Unmentioned codes are considered to map to 0.
(2) a list (or a tuple) with three numbers, denoting the sizes of the
regions in the following order: (10, 01, 11) and (3) a list containing
the subsets of values.
The subsets can be a list (or a tuple) containing two set objects. For
instance:
.. plot::
:include-source:
from sequana.viz.venn import plot_venn
A = set([1,2,3,4,5,6,7,8,9])
B = set([ 7,8,9,10,11])
plot_venn((A, B), labels=("A", "B"))
This is the unweighted version by default meaning all circles have the same
size. If you prefer to have circle scaled to the
size of the sets, add the relevant parameter as follows:
.. plot::
:include-source:
from sequana.viz.venn import plot_venn
A = set([1,2,3,4,5,6,7,8,9])
B = set([ 7,8,9,10,11])
plot_venn((A, B), labels=("A", "B"), weighted=True)
Similarly for 3 sets, a Venn diagram can be represented as follows. Note
here that we also use the *title* parameter:
.. plot::
:include-source:
from sequana.viz.venn import plot_venn
A = set([1,2,3,4,5,6,7,8,9])
B = set([ 4,5,6,7,8,9,10,11,12,13])
C = set([ 3,4,5,6,7,8,9])
plot_venn((A, B, C), labels=("A", "B", "C"), title="my Venn3 diagram")
Input can be a list/tuple of 2 or 3 sets as described above.
"""
if isinstance(subsets, (list, tuple)):
n_sets = len(subsets)
data = get_labels(subsets)
elif isinstance(subsets, dict):
n_sets = len(list(subsets.keys())[0])
data = subsets
venn_func_name = f"venn{n_sets}"
try:
venn_func = globals().get(venn_func_name)
if not venn_func:
raise ValueError(f"Venn diagram for {n_sets} sets is not supported.")
venn = venn_func(data, names=labels)
if title:
pylab.title(title)
except Exception as e:
print(f"Error: {e}")
