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_chord_diagram.py
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"""
https://github.com/fengwangPhysics/matplotlib-chord-diagram/blob/master/matplotlib-chord.py
With modifications
"""
from typing import List, Union, Tuple
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.path import Path
import matplotlib.patches as patches
import seaborn as sns
import numpy as np
import pandas as pd
Axis = Union[matplotlib.axes.Axes]
Array = Union[np.ndarray]
DataFrame = Union[pd.DataFrame]
LW = 0.3
def chord_diagram(
X: Union[Array, DataFrame],
ax: Axis = None,
palette: str = "tab20",
width: float = 0.1,
pad: float = 2,
chordwidth: float = 0.7,
labels: List[str] = None,
) -> Array:
"""Plot a chord diagram
Parameters
----------
X :
flux data, X[i, j] is the flux from i to j
ax :
matplotlib `axes` to show the plot
colors : optional
user defined colors in rgb format. Use function hex2rgb() to convert hex color to rgb color. Default: d3.js category10
width : optional
width/thickness of the ideogram arc
pad : optional
gap pad between two neighboring ideogram arcs, unit: degree, default: 2 degree
chordwidth : optional
position of the control points for the chords, controlling the shape of the chords
"""
if isinstance(X, pd.DataFrame) and labels is None:
labels = X.index
X = X.values
if ax is None:
fig, ax = plt.subplots(figsize=(5, 5))
# X[i, j]: i -> j
x = X.sum(axis=1) # sum over rows
if (x == 0).any():
X = X + 1e-30
x = X.sum(axis=1)
ax.set_xlim(-1.1, 1.1)
ax.set_ylim(-1.1, 1.1)
colors = sns.color_palette(palette, len(x))
# find position for each start and end
y = x / np.sum(x).astype(float) * (360 - pad * len(x))
pos = {}
arc = []
nodePos = []
start = 0
for i in range(len(x)):
end = start + y[i]
arc.append((start, end))
angle = 0.5 * (start + end)
# print(start, end, angle)
if -30 <= angle <= 210:
angle -= 90
else:
angle -= 270
nodePos.append(
tuple(polar2xy(1.1, 0.5 * (start + end) * np.pi / 180.0)) + (angle,)
)
z = (X[i, :] / x[i].astype(float)) * (end - start)
ids = np.argsort(z)
z0 = start
for j in ids:
pos[(i, j)] = (z0, z0 + z[j])
z0 += z[j]
start = end + pad
for i in range(len(x)):
start, end = arc[i]
ideogram_arc(
start=start,
end=end,
radius=1.0,
ax=ax,
color=colors[i],
width=width,
)
start, end = pos[(i, i)]
self_chord_arc(
start,
end,
radius=1.0 - width,
color=colors[i],
chordwidth=chordwidth * 0.7,
ax=ax,
)
for j in range(i):
color = colors[i]
if X[i, j] > X[j, i]:
color = colors[j]
start1, end1 = pos[(i, j)]
start2, end2 = pos[(j, i)]
chord_arc(
start1,
end1,
start2,
end2,
radius=1.0 - width,
color=colors[i],
chordwidth=chordwidth,
ax=ax,
)
ax.axis("off")
if labels is not None:
prop = dict(fontsize=16 * 0.8, ha="center", va="center")
for i, label in enumerate(labels):
ax.text(
nodePos[i][0],
nodePos[i][1],
label,
rotation=nodePos[i][2],
**prop
)
if "fig" in locals():
return fig
def polar2xy(r: float, theta: float) -> Array:
return np.array([r * np.cos(theta), r * np.sin(theta)])
def hex2rgb(c: str) -> Tuple[float, float, float]:
return tuple(int(c[i : i + 2], 16) / 256.0 for i in (1, 3, 5)) # type: ignore[return-value]
def ideogram_arc(
start=0, end=60, radius=1.0, width=0.2, ax=None, color=(1, 0, 0)
):
# start, end should be in [0, 360)
if start > end:
start, end = end, start
start *= np.pi / 180.0
end *= np.pi / 180.0
# optimal distance to the control points
# https://stackoverflow.com/questions/1734745/how-to-create-circle-with-b%C3%A9zier-curves
opt = 4.0 / 3.0 * np.tan((end - start) / 4.0) * radius
inner = radius * (1 - width)
verts = [
polar2xy(radius, start),
polar2xy(radius, start) + polar2xy(opt, start + 0.5 * np.pi),
polar2xy(radius, end) + polar2xy(opt, end - 0.5 * np.pi),
polar2xy(radius, end),
polar2xy(inner, end),
polar2xy(inner, end) + polar2xy(opt * (1 - width), end - 0.5 * np.pi),
polar2xy(inner, start)
+ polar2xy(opt * (1 - width), start + 0.5 * np.pi),
polar2xy(inner, start),
polar2xy(radius, start),
]
codes = [
Path.MOVETO,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.LINETO,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CLOSEPOLY,
]
if ax == None:
return verts, codes
else:
path = Path(verts, codes)
patch = patches.PathPatch(
path, facecolor=color + (0.5,), edgecolor=color + (0.4,), lw=LW
)
ax.add_patch(patch)
def chord_arc(
start1=0,
end1=60,
start2=180,
end2=240,
radius=1.0,
chordwidth=0.7,
ax=None,
color=(1, 0, 0),
):
# start, end should be in [0, 360)
if start1 > end1:
start1, end1 = end1, start1
if start2 > end2:
start2, end2 = end2, start2
start1 *= np.pi / 180.0
end1 *= np.pi / 180.0
start2 *= np.pi / 180.0
end2 *= np.pi / 180.0
opt1 = 4.0 / 3.0 * np.tan((end1 - start1) / 4.0) * radius
opt2 = 4.0 / 3.0 * np.tan((end2 - start2) / 4.0) * radius
rchord = radius * (1 - chordwidth)
verts = [
polar2xy(radius, start1),
polar2xy(radius, start1) + polar2xy(opt1, start1 + 0.5 * np.pi),
polar2xy(radius, end1) + polar2xy(opt1, end1 - 0.5 * np.pi),
polar2xy(radius, end1),
polar2xy(rchord, end1),
polar2xy(rchord, start2),
polar2xy(radius, start2),
polar2xy(radius, start2) + polar2xy(opt2, start2 + 0.5 * np.pi),
polar2xy(radius, end2) + polar2xy(opt2, end2 - 0.5 * np.pi),
polar2xy(radius, end2),
polar2xy(rchord, end2),
polar2xy(rchord, start1),
polar2xy(radius, start1),
]
codes = [
Path.MOVETO,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
]
if ax == None:
return verts, codes
else:
path = Path(verts, codes)
patch = patches.PathPatch(
path, facecolor=color + (0.5,), edgecolor=color + (0.4,), lw=LW
)
ax.add_patch(patch)
def self_chord_arc(
start=0, end=60, radius=1.0, chordwidth=0.7, ax=None, color=(1, 0, 0)
):
# start, end should be in [0, 360)
if start > end:
start, end = end, start
start *= np.pi / 180.0
end *= np.pi / 180.0
opt = 4.0 / 3.0 * np.tan((end - start) / 4.0) * radius
rchord = radius * (1 - chordwidth)
verts = [
polar2xy(radius, start),
polar2xy(radius, start) + polar2xy(opt, start + 0.5 * np.pi),
polar2xy(radius, end) + polar2xy(opt, end - 0.5 * np.pi),
polar2xy(radius, end),
polar2xy(rchord, end),
polar2xy(rchord, start),
polar2xy(radius, start),
]
codes = [
Path.MOVETO,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
]
if ax == None:
return verts, codes
else:
path = Path(verts, codes)
patch = patches.PathPatch(
path, facecolor=color + (0.5,), edgecolor=color + (0.4,), lw=LW
)
ax.add_patch(patch)