PCA example with Iris Data-set¶

Principal Component Analysis applied to the Iris dataset.

See here for more information on this dataset.

# Code source: Gaël Varoquaux
# License: BSD 3 clause

import matplotlib.pyplot as plt

# unused but required import for doing 3d projections with matplotlib < 3.2
import mpl_toolkits.mplot3d  # noqa: F401
import numpy as np

from sklearn import datasets, decomposition

np.random.seed(5)

iris = datasets.load_iris()
X = iris.data
y = iris.target

fig = plt.figure(1, figsize=(4, 3))
plt.clf()

ax = fig.add_subplot(111, projection="3d", elev=48, azim=134)
ax.set_position([0, 0, 0.95, 1])


plt.cla()
pca = decomposition.PCA(n_components=3)
pca.fit(X)
X = pca.transform(X)

for name, label in [("Setosa", 0), ("Versicolour", 1), ("Virginica", 2)]:
    ax.text3D(
        X[y == label, 0].mean(),
        X[y == label, 1].mean() + 1.5,
        X[y == label, 2].mean(),
        name,
        horizontalalignment="center",
        bbox=dict(alpha=0.5, edgecolor="w", facecolor="w"),
    )
# Reorder the labels to have colors matching the cluster results
y = np.choose(y, [1, 2, 0]).astype(float)
ax.scatter(X[:, 0], X[:, 1], X[:, 2], c=y, cmap=plt.cm.nipy_spectral, edgecolor="k")

ax.xaxis.set_ticklabels([])
ax.yaxis.set_ticklabels([])
ax.zaxis.set_ticklabels([])

plt.show()