PCA Application Notebook Summary
This notebook demonstrates how Principal Component Analysis (PCA) converts high-dimensional datasets into lower-dimensional visualizations while preserving structure and class separation.
PCA for high-dimensional image data
- Uses the MNIST dataset with
784input features - Reduces the data to
2principal components - Plots a 2D scatter of digit clusters, making digit categories easier to see
PCA for 3D data visualization
- Generates the
Swiss Rolldataset - Reduces from
3Dto2D - Shows how PCA “unrolls” complex 3D structure into a flat, interpretable view
PCA for the classic Iris dataset
- Starts with
4Dflower measurement data - Demonstrates both:
4D → 1Dprojection with class-colored points4D → 2Dprojection for direct cluster separation
- Also includes an interactive
4D → 3DPlotly visualization
Why this matters
- Highlights PCA as a key technique for:
- dimensionality reduction
- exploratory data analysis
- visualizing complex datasets
- understanding how features relate to class structure
Principal Component Analysis: Application¶
Using PCA to reduce dimension to visualize¶
If there are a large number of variables or dimensions along which the data is distributed, which is common in real world , visualization can be a challenge and almost impossible. Hence, PCA can do that for you since it projects the data into a lower dimension, thereby allowing you to visualize the data in a 2D or 3D space with a naked eye.
784 dimension data to 2 dimension¶
In [1]:
from sklearn.decomposition import PCA
import matplotlib.pyplot as plt
from sklearn.datasets import fetch_openml
import numpy as np
X, y = fetch_openml('mnist_784', version=1,
return_X_y=True, as_frame=False)
print(X.shape) # has 784 dimension
(70000, 784)
In [2]:
# Lets see 1st data
np.set_printoptions(linewidth=115)
print(X[0])
[ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 18 18 18 126 136 175 26 166 255 247 127 0 0 0 0 0 0 0 0 0 0 0 0 30 36 94 154 170 253 253 253 253 253 225 172 253 242 195 64 0 0 0 0 0 0 0 0 0 0 0 49 238 253 253 253 253 253 253 253 253 251 93 82 82 56 39 0 0 0 0 0 0 0 0 0 0 0 0 18 219 253 253 253 253 253 198 182 247 241 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 156 107 253 253 205 11 0 43 154 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 1 154 253 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 139 253 190 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 190 253 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 241 225 160 108 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 81 240 253 253 119 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 186 253 253 150 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 93 252 253 187 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 249 253 249 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 46 130 183 253 253 207 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 148 229 253 253 253 250 182 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 114 221 253 253 253 253 201 78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 66 213 253 253 253 253 198 81 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 171 219 253 253 253 253 195 80 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 172 226 253 253 253 253 244 133 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 253 253 253 212 135 132 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
In [3]:
# Create PCA with 2 components
pca = PCA(n_components=2)
X_pca = pca.fit_transform(X)
In [4]:
# lets print 1st data
print("X original :", X[0])
print("X with PCA=2:", X_pca[0])
X original : [ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 18 18 18 126 136 175 26 166 255 247 127 0 0 0 0 0 0 0 0 0 0 0 0 30 36 94 154 170 253 253 253 253 253 225 172 253 242 195 64 0 0 0 0 0 0 0 0 0 0 0 49 238 253 253 253 253 253 253 253 253 251 93 82 82 56 39 0 0 0 0 0 0 0 0 0 0 0 0 18 219 253 253 253 253 253 198 182 247 241 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 156 107 253 253 205 11 0 43 154 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 1 154 253 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 139 253 190 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 190 253 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 241 225 160 108 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 81 240 253 253 119 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 186 253 253 150 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 93 252 253 187 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 249 253 249 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 46 130 183 253 253 207 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 148 229 253 253 253 250 182 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 114 221 253 253 253 253 201 78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 66 213 253 253 253 253 198 81 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 171 219 253 253 253 253 195 80 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 172 226 253 253 253 253 244 133 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 253 253 253 212 135 132 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0] X with PCA=2: [ 122.24857361 -316.20802996]
In [24]:
# Plot 2D scatter
plt.figure(figsize=(10,7))
plt.scatter(X_pca[:,0], X_pca[:,1], c=y.astype(int),
cmap='tab10', s=2)
plt.colorbar()
plt.title("MNIST PCA - 2 Components")
plt.show()
It is somewhat easier to see the 10 different digits.
In [ ]:
In [ ]:
3 dimension data to 2 dimension¶
In [5]:
import matplotlib.pyplot as plt
from sklearn.datasets import make_swiss_roll
from sklearn.decomposition import PCA
# Generate dataset
X, color = make_swiss_roll(n_samples=2000, noise=0.2)
print(X.shape) # 3 dimension data
(2000, 3)
In [6]:
# Lets see 1st data
print(X[0])
[ 6.6436887 16.51102643 -9.91622573]
In [7]:
# Apply PCA
pca = PCA(n_components=2)
X_pca = pca.fit_transform(X)
# lets print 1st data
print(X_pca[0])
[-6.30734299 9.26597758]
In [18]:
# Plot original 3D Swiss Roll
fig = plt.figure(figsize=(13, 5))
ax = fig.add_subplot(1, 2, 1, projection='3d')
ax.scatter(X[:,0], X[:,1], X[:,2], c=color, cmap='viridis')
ax.set_title("Original 3D Swiss Roll")
# Plot 2D PCA visualization
plt.subplot(1, 2, 2)
plt.scatter(X_pca[:,0], X_pca[:,1], c=color, cmap='viridis')
plt.title("2D PCA Unrolled Swiss Roll")
plt.show()
This is what the data looks like in 3D: complex and curled.
After PCA, it becomes 2D: flattened and easy to understand.
In [ ]:
4 dimension to 2 dimension: Iris Dataset¶
In [8]:
import matplotlib.pyplot as plt
from sklearn.datasets import load_iris
from sklearn.decomposition import PCA
# Load Iris dataset
iris = load_iris()
X = iris.data # (150, 4)
y = iris.target # class labels
labels = iris.target_names # class names
print(X.shape)
(150, 4)
In [9]:
X
Out[9]:
array([[5.1, 3.5, 1.4, 0.2],
[4.9, 3. , 1.4, 0.2],
[4.7, 3.2, 1.3, 0.2],
[4.6, 3.1, 1.5, 0.2],
[5. , 3.6, 1.4, 0.2],
[5.4, 3.9, 1.7, 0.4],
[4.6, 3.4, 1.4, 0.3],
[5. , 3.4, 1.5, 0.2],
[4.4, 2.9, 1.4, 0.2],
[4.9, 3.1, 1.5, 0.1],
[5.4, 3.7, 1.5, 0.2],
[4.8, 3.4, 1.6, 0.2],
[4.8, 3. , 1.4, 0.1],
[4.3, 3. , 1.1, 0.1],
[5.8, 4. , 1.2, 0.2],
[5.7, 4.4, 1.5, 0.4],
[5.4, 3.9, 1.3, 0.4],
[5.1, 3.5, 1.4, 0.3],
[5.7, 3.8, 1.7, 0.3],
[5.1, 3.8, 1.5, 0.3],
[5.4, 3.4, 1.7, 0.2],
[5.1, 3.7, 1.5, 0.4],
[4.6, 3.6, 1. , 0.2],
[5.1, 3.3, 1.7, 0.5],
[4.8, 3.4, 1.9, 0.2],
[5. , 3. , 1.6, 0.2],
[5. , 3.4, 1.6, 0.4],
[5.2, 3.5, 1.5, 0.2],
[5.2, 3.4, 1.4, 0.2],
[4.7, 3.2, 1.6, 0.2],
[4.8, 3.1, 1.6, 0.2],
[5.4, 3.4, 1.5, 0.4],
[5.2, 4.1, 1.5, 0.1],
[5.5, 4.2, 1.4, 0.2],
[4.9, 3.1, 1.5, 0.2],
[5. , 3.2, 1.2, 0.2],
[5.5, 3.5, 1.3, 0.2],
[4.9, 3.6, 1.4, 0.1],
[4.4, 3. , 1.3, 0.2],
[5.1, 3.4, 1.5, 0.2],
[5. , 3.5, 1.3, 0.3],
[4.5, 2.3, 1.3, 0.3],
[4.4, 3.2, 1.3, 0.2],
[5. , 3.5, 1.6, 0.6],
[5.1, 3.8, 1.9, 0.4],
[4.8, 3. , 1.4, 0.3],
[5.1, 3.8, 1.6, 0.2],
[4.6, 3.2, 1.4, 0.2],
[5.3, 3.7, 1.5, 0.2],
[5. , 3.3, 1.4, 0.2],
[7. , 3.2, 4.7, 1.4],
[6.4, 3.2, 4.5, 1.5],
[6.9, 3.1, 4.9, 1.5],
[5.5, 2.3, 4. , 1.3],
[6.5, 2.8, 4.6, 1.5],
[5.7, 2.8, 4.5, 1.3],
[6.3, 3.3, 4.7, 1.6],
[4.9, 2.4, 3.3, 1. ],
[6.6, 2.9, 4.6, 1.3],
[5.2, 2.7, 3.9, 1.4],
[5. , 2. , 3.5, 1. ],
[5.9, 3. , 4.2, 1.5],
[6. , 2.2, 4. , 1. ],
[6.1, 2.9, 4.7, 1.4],
[5.6, 2.9, 3.6, 1.3],
[6.7, 3.1, 4.4, 1.4],
[5.6, 3. , 4.5, 1.5],
[5.8, 2.7, 4.1, 1. ],
[6.2, 2.2, 4.5, 1.5],
[5.6, 2.5, 3.9, 1.1],
[5.9, 3.2, 4.8, 1.8],
[6.1, 2.8, 4. , 1.3],
[6.3, 2.5, 4.9, 1.5],
[6.1, 2.8, 4.7, 1.2],
[6.4, 2.9, 4.3, 1.3],
[6.6, 3. , 4.4, 1.4],
[6.8, 2.8, 4.8, 1.4],
[6.7, 3. , 5. , 1.7],
[6. , 2.9, 4.5, 1.5],
[5.7, 2.6, 3.5, 1. ],
[5.5, 2.4, 3.8, 1.1],
[5.5, 2.4, 3.7, 1. ],
[5.8, 2.7, 3.9, 1.2],
[6. , 2.7, 5.1, 1.6],
[5.4, 3. , 4.5, 1.5],
[6. , 3.4, 4.5, 1.6],
[6.7, 3.1, 4.7, 1.5],
[6.3, 2.3, 4.4, 1.3],
[5.6, 3. , 4.1, 1.3],
[5.5, 2.5, 4. , 1.3],
[5.5, 2.6, 4.4, 1.2],
[6.1, 3. , 4.6, 1.4],
[5.8, 2.6, 4. , 1.2],
[5. , 2.3, 3.3, 1. ],
[5.6, 2.7, 4.2, 1.3],
[5.7, 3. , 4.2, 1.2],
[5.7, 2.9, 4.2, 1.3],
[6.2, 2.9, 4.3, 1.3],
[5.1, 2.5, 3. , 1.1],
[5.7, 2.8, 4.1, 1.3],
[6.3, 3.3, 6. , 2.5],
[5.8, 2.7, 5.1, 1.9],
[7.1, 3. , 5.9, 2.1],
[6.3, 2.9, 5.6, 1.8],
[6.5, 3. , 5.8, 2.2],
[7.6, 3. , 6.6, 2.1],
[4.9, 2.5, 4.5, 1.7],
[7.3, 2.9, 6.3, 1.8],
[6.7, 2.5, 5.8, 1.8],
[7.2, 3.6, 6.1, 2.5],
[6.5, 3.2, 5.1, 2. ],
[6.4, 2.7, 5.3, 1.9],
[6.8, 3. , 5.5, 2.1],
[5.7, 2.5, 5. , 2. ],
[5.8, 2.8, 5.1, 2.4],
[6.4, 3.2, 5.3, 2.3],
[6.5, 3. , 5.5, 1.8],
[7.7, 3.8, 6.7, 2.2],
[7.7, 2.6, 6.9, 2.3],
[6. , 2.2, 5. , 1.5],
[6.9, 3.2, 5.7, 2.3],
[5.6, 2.8, 4.9, 2. ],
[7.7, 2.8, 6.7, 2. ],
[6.3, 2.7, 4.9, 1.8],
[6.7, 3.3, 5.7, 2.1],
[7.2, 3.2, 6. , 1.8],
[6.2, 2.8, 4.8, 1.8],
[6.1, 3. , 4.9, 1.8],
[6.4, 2.8, 5.6, 2.1],
[7.2, 3. , 5.8, 1.6],
[7.4, 2.8, 6.1, 1.9],
[7.9, 3.8, 6.4, 2. ],
[6.4, 2.8, 5.6, 2.2],
[6.3, 2.8, 5.1, 1.5],
[6.1, 2.6, 5.6, 1.4],
[7.7, 3. , 6.1, 2.3],
[6.3, 3.4, 5.6, 2.4],
[6.4, 3.1, 5.5, 1.8],
[6. , 3. , 4.8, 1.8],
[6.9, 3.1, 5.4, 2.1],
[6.7, 3.1, 5.6, 2.4],
[6.9, 3.1, 5.1, 2.3],
[5.8, 2.7, 5.1, 1.9],
[6.8, 3.2, 5.9, 2.3],
[6.7, 3.3, 5.7, 2.5],
[6.7, 3. , 5.2, 2.3],
[6.3, 2.5, 5. , 1.9],
[6.5, 3. , 5.2, 2. ],
[6.2, 3.4, 5.4, 2.3],
[5.9, 3. , 5.1, 1.8]])
In [26]:
# Lets see 1st data
print(X[0])
[5.1 3.5 1.4 0.2]
In [16]:
# Reduce 4D Iris data to 1D and plot colored by class
pca_1d = PCA(n_components=1)
X_pca_1d = pca_1d.fit_transform(X)
# lets print 1st data
print(X[0],"-->" ,X_pca_1d[0])
plt.figure(figsize=(10, 2))
for i, label in enumerate(labels):
plt.scatter(
X_pca_1d[y == i, 0],
np.zeros(np.sum(y == i)),
label=label,
s=40,
alpha=0.7
)
plt.yticks([])
plt.xlabel("Principal Component 1")
plt.title("Iris Dataset PCA (4D → 1D)")
plt.legend()
plt.grid(axis='x', linestyle='--', alpha=0.4)
plt.show()
[5.1 3.5 1.4 0.2] --> [-2.68412563]
In [ ]:
In [18]:
# Apply PCA → reduce 4D → 2D
pca_2d = PCA(n_components=2)
X_pca_2d = pca_2d.fit_transform(X)
# lets print 1st data
print(X[0], "-->", X_pca_2d[0])
# Plot
plt.figure(figsize=(8, 6))
for i, label in enumerate(labels):
plt.scatter(
X_pca_2d[y == i, 0],
X_pca_2d[y == i, 1],
label=label
)
plt.xlabel("Principal Component 1")
plt.ylabel("Principal Component 2")
plt.title("Iris Dataset PCA (4D → 2D)")
plt.legend()
plt.grid(True)
plt.show()
[5.1 3.5 1.4 0.2] --> [-2.68412563 0.31939725]
In [ ]:
In [20]:
# 4D to 3D PCA visualization with Plotly Express
import plotly.express as px
import pandas as pd
from sklearn.decomposition import PCA
# 1. Reduce dimensions to 3D
pca_3d = PCA(n_components=3)
X_pca_3d = pca_3d.fit_transform(X)
print(X_pca_3d.shape)
print(X[0], "-->", X_pca_3d[0])
# 2. Convert data to a DataFrame for Plotly Express
# Maps target integer array 'y' to the textual labels
mapped_labels = [labels[i] for i in y]
df_pca = pd.DataFrame(X_pca_3d, columns=['PC1', 'PC2', 'PC3'])
df_pca['Species'] = mapped_labels
# 3. Create interactive 3D plot
fig = px.scatter_3d(
df_pca,
x='PC1',
y='PC2',
z='PC3',
color='Species',
title="Iris Dataset PCA (4D → 3D)",
labels={
'PC1': 'Principal Component 1',
'PC2': 'Principal Component 2',
'PC3': 'Principal Component 3'
}
)
# 4. Adjust layout sizing
fig.update_layout(width=800, height=600)
fig.show()
(150, 3) [5.1 3.5 1.4 0.2] --> [-2.68412563 0.31939725 -0.02791483]
In [ ]: