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@tboggs
Last active July 10, 2024 13:49
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A script to generate contour plots of Dirichlet distributions
'''Functions for drawing contours of Dirichlet distributions.
MIT License
Copyright (c) 2014 Thomas Boggs
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
'''
from __future__ import division, print_function
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.tri as tri
_corners = np.array([[0, 0], [1, 0], [0.5, 0.75**0.5]])
_AREA = 0.5 * 1 * 0.75**0.5
_triangle = tri.Triangulation(_corners[:, 0], _corners[:, 1])
# For each corner of the triangle, the pair of other corners
_pairs = [_corners[np.roll(range(3), -i)[1:]] for i in range(3)]
# The area of the triangle formed by point xy and another pair or points
tri_area = lambda xy, pair: 0.5 * np.linalg.norm(np.cross(*(pair - xy)))
def xy2bc(xy, tol=1.e-4):
'''Converts 2D Cartesian coordinates to barycentric.
Arguments:
`xy`: A length-2 sequence containing the x and y value.
'''
coords = np.array([tri_area(xy, p) for p in _pairs]) / _AREA
return np.clip(coords, tol, 1.0 - tol)
class Dirichlet(object):
def __init__(self, alpha):
'''Creates Dirichlet distribution with parameter `alpha`.'''
from math import gamma
from operator import mul
self._alpha = np.array(alpha)
self._coef = gamma(np.sum(self._alpha)) / \
np.multiply.reduce([gamma(a) for a in self._alpha])
def pdf(self, x):
'''Returns pdf value for `x`.'''
from operator import mul
return self._coef * np.multiply.reduce([xx ** (aa - 1)
for (xx, aa)in zip(x, self._alpha)])
def sample(self, N):
'''Generates a random sample of size `N`.'''
return np.random.dirichlet(self._alpha, N)
def draw_pdf_contours(dist, border=False, nlevels=200, subdiv=8, **kwargs):
'''Draws pdf contours over an equilateral triangle (2-simplex).
Arguments:
`dist`: A distribution instance with a `pdf` method.
`border` (bool): If True, the simplex border is drawn.
`nlevels` (int): Number of contours to draw.
`subdiv` (int): Number of recursive mesh subdivisions to create.
kwargs: Keyword args passed on to `plt.triplot`.
'''
from matplotlib import ticker, cm
import math
refiner = tri.UniformTriRefiner(_triangle)
trimesh = refiner.refine_triangulation(subdiv=subdiv)
pvals = [dist.pdf(xy2bc(xy)) for xy in zip(trimesh.x, trimesh.y)]
plt.tricontourf(trimesh, pvals, nlevels, cmap='jet', **kwargs)
plt.axis('equal')
plt.xlim(0, 1)
plt.ylim(0, 0.75**0.5)
plt.axis('off')
if border is True:
plt.triplot(_triangle, linewidth=1)
def plot_points(X, barycentric=True, border=True, **kwargs):
'''Plots a set of points in the simplex.
Arguments:
`X` (ndarray): A 2xN array (if in Cartesian coords) or 3xN array
(if in barycentric coords) of points to plot.
`barycentric` (bool): Indicates if `X` is in barycentric coords.
`border` (bool): If True, the simplex border is drawn.
kwargs: Keyword args passed on to `plt.plot`.
'''
if barycentric is True:
X = X.dot(_corners)
plt.plot(X[:, 0], X[:, 1], 'k.', ms=1, **kwargs)
plt.axis('equal')
plt.xlim(0, 1)
plt.ylim(0, 0.75**0.5)
plt.axis('off')
if border is True:
plt.triplot(_triangle, linewidth=1)
if __name__ == '__main__':
f = plt.figure(figsize=(8, 6))
alphas = [[0.999] * 3,
[5] * 3,
[2, 5, 15]]
for (i, alpha) in enumerate(alphas):
plt.subplot(2, len(alphas), i + 1)
dist = Dirichlet(alpha)
draw_pdf_contours(dist)
title = r'$\alpha$ = (%.3f, %.3f, %.3f)' % tuple(alpha)
plt.title(title, fontdict={'fontsize': 8})
plt.subplot(2, len(alphas), i + 1 + len(alphas))
plot_points(dist.sample(5000))
plt.savefig('dirichlet_plots.png')
print('Wrote plots to "dirichlet_plots.png".')
@valo
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valo commented Mar 25, 2014

Very strange. I have matplotlib 1.3.1 and I get this error:

Traceback (most recent call last):
  File "simplex_plots.py", line 106, in <module>
    draw_pdf_contours(dist)
  File "simplex_plots.py", line 60, in draw_pdf_contours
    refiner = tri.trirefine.UniformTriRefiner(_triangle)
AttributeError: 'module' object has no attribute 'trirefine'

@tboggs
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tboggs commented Jul 2, 2014

This is a late reply because - for some reason - I never received notification of your comment. Did you edit the code before running? I ask because the line referenced in your error (line 60) doesn't match what is in my code. Your line is

refiner = tri.trirefine.UniformTriRefiner(_triangle)

which has an extra trirefine submodule referenced. The line in my code is just

refiner = tri.UniformTriRefiner(_triangle)

@aloctavodia
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Hi,

For those using Python 3. You should do:

from functools import reduce

@mlandnlp
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Thank you for creating the script and helping me build more intuition for the Dirichlet Distribution :-)

@tboggs
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tboggs commented Apr 18, 2020

It came to my attention that the function xy2bc was incorrect, which resulted in varying inaccuracy over the simplex. While it didn't appear to make a difference for the tolerance used, I've updated this gist with a corrected implementation that uses fractional triangle areas to compute the barycentric coordinates. I also made some minor edits to account for python and matplotlib API changes since the original post.

@willfrew
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Really useful - thanks!

@kwahcarioca
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kwahcarioca commented Aug 29, 2023

Your code is very nice showing how to implement Dirichlet straight from the formula. I ve also tried to experiment it calling scipy.stats.dirichlet library instead. It worked well but we needed to change the tolerance of the xy2bc generator from 1e-4 to 1e-9. Otherwise the assertion of the library code _multivariate.py wont let us to run.
if (np.abs(np.sum(x, 0) - 1.0) > 10e-10).any():
raise ValueError("The input vector 'x' must lie within the normal "
"simplex. but np.sum(x, 0) = %s." % np.sum(x, 0))

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