Principal Component Analysis

Principal component analysis (PCA) is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components.

[Source: Wikipedia]

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D

from sklearn import decomposition

X=pd.get_dummies(df.loc[:, ['sepal_length', 'sepal_width','petal_length','petal_width']])
y=df.loc[:, 'species']

print("Original:\n %s" % X.head())

pca = decomposition.PCA(n_components=3)
X = pca.transform(X)
X = pd.DataFrame(X,columns=["1st PC","2nd PC","3rd PC"])
print("Transformed:\n %s" % X.head())

colorDict =	{ "setosa": "r", "virginica": "g","versicolor": "b" }
def applyColor(idx):
	return colorDict[idx]

X["Species"] = y
X["Color"] = X.Species.apply(applyColor)

fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(X["1st PC"], X["2nd PC"], X["3rd PC"], c=X["Color"], s=60)
ax.view_init(30, 185)