MDS.py

import numpy as np
import matplotlib.pyplot as plt
from sklearn import manifold
%matplotlib inline

D = np.array([[0, 10, 6], [10, 0, 5], [6, 5, 0]])

M = manifold.MDS(n_components=2, n_init=1, max_iter=10000, metric=True, dissimilarity="precomputed")
K = M.fit_transform(D)
print("Stress", M.stress_)

fig = plt.figure()
ax = fig.add_subplot(111)
ax.patch.set_facecolor('white')
ax.scatter(K[...,0], K[...,1], c=("red", "green", "blue"), s=120, edgecolors='none')
ax.set_autoscale_on(False)
ax.axis('square')

ax.set_xlabel('R1')
ax.set_ylabel('R2')
fig.suptitle("MDS")
plt.show()