pcabreastcancer.py

# -*- coding: utf-8 -*-

from __future__ import print_function
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import PCA
from sklearn.naive_bayes import GaussianNB
from sklearn import metrics
import matplotlib.pyplot as plt
from sklearn.datasets import load_breast_cancer
from sklearn.pipeline import make_pipeline


RANDOM_STATE = 42
FIG_SIZE = (10, 7)


features, target = load_breast_cancer(return_X_y=True)

# Make a train/test split using 30% test size
X_train, X_test, y_train, y_test = train_test_split(features, target,
                                                    test_size=0.30,
                                                    random_state=RANDOM_STATE)

# Fit to data and predict using pipelined GNB and PCA.
unscaled_clf = make_pipeline(PCA(n_components=2), GaussianNB())
unscaled_clf.fit(X_train, y_train)
pred_test = unscaled_clf.predict(X_test)

# Fit to data and predict using pipelined scaling, GNB and PCA.
std_clf = make_pipeline(StandardScaler(), PCA(n_components=2), GaussianNB())
std_clf.fit(X_train, y_train)
pred_test_std = std_clf.predict(X_test)

# Show prediction accuracies in scaled and unscaled data.
print('\nPrediction accuracy for the normal test dataset with PCA')
print('{:.2%}\n'.format(metrics.accuracy_score(y_test, pred_test)))

print('\nPrediction accuracy for the standardized test dataset with PCA')
print('{:.2%}\n'.format(metrics.accuracy_score(y_test, pred_test_std)))

# Extract PCA from pipeline
pca = unscaled_clf.named_steps['pca']
pca_std = std_clf.named_steps['pca']

# Show first principal componenets
print('\nPC 1 without scaling:\n', pca.components_[0])
print('\nPC 1 with scaling:\n', pca_std.components_[0])

# Scale and use PCA on X_train data for visualization.
scaler = std_clf.named_steps['standardscaler']
X_train_std = pca_std.transform(scaler.transform(X_train))

# visualize standardized vs. untouched dataset with PCA performed
fig, (ax1, ax2) = plt.subplots(ncols=2, figsize=FIG_SIZE)


for l, c, m in zip(range(0, 3), ('blue', 'red', 'green'), ('^', 's', 'o')):
    ax1.scatter(X_train[y_train == l, 0], X_train[y_train == l, 1],
                color=c,
                label='class %s' % l,
                alpha=0.5,
                marker=m
                )

for l, c, m in zip(range(0, 3), ('blue', 'red', 'green'), ('^', 's', 'o')):
    ax2.scatter(X_train_std[y_train == l, 0], X_train_std[y_train == l, 1],
                color=c,
                label='class %s' % l,
                alpha=0.5,
                marker=m
                )

ax1.set_title('Training dataset after PCA')
ax2.set_title('Standardized training dataset after PCA')

for ax in (ax1, ax2):
    ax.set_xlabel('1st principal component')
    ax.set_ylabel('2nd principal component')
    ax.legend(loc='upper right')
    ax.grid()

plt.tight_layout()

plt.show()