Matplotlib

Matplotlib - Data Visualization

The most widely used library for 2D (and basic 3D) plotting. It provides full control over every element of a figure, from line styles to axis spines.

When to Use

• Creating publication-quality 2D plots (Line, Scatter, Bar, Hist)
• Visualizing scientific data (Heatmaps, Contours, Vector fields)
• Generating complex multi-panel figures
• Fine-tuning plots for papers/reports (LaTeX support)
• Building custom visualization tools and dashboards
• Plotting data directly from NumPy arrays or Pandas DataFrames

Reference Documentation

Official docs: https://matplotlib.org/stable/index.html Gallery: https://matplotlib.org/stable/gallery/index.html (Essential for finding examples) Search patterns: plt.subplots, ax.set_title, ax.legend, plt.savefig, matplotlib.colors

Core Principles

Two Interfaces: Choose Wisely

Use Matplotlib For

• High-level control over figure layout.
• Precise styling for publication.
• Embedding plots in GUI applications.

Do NOT Use For

• Interactive web dashboards (use Plotly or Bokeh).
• Rapid statistical exploration (use Seaborn — it's built on Matplotlib but simpler for stats).
• Very large datasets (>1M points) in real-time (use Datashader or VisPy).

Quick Reference

Installation

pip install matplotlib

Standard Imports

import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from matplotlib import gridspec

Basic Pattern - The OO Interface (The "Proper" Way)

import matplotlib.pyplot as plt
import numpy as np

x = np.linspace(0, 10, 100)
y = np.sin(x)

# 1. Create Figure and Axis objects
fig, ax = plt.subplots(figsize=(8, 5))

# 2. Plot data
ax.plot(x, y, label='Sine Wave', color='tab:blue', linewidth=2)

# 3. Customize
ax.set_xlabel('Time (s)')
ax.set_ylabel('Amplitude')
ax.set_title('Oscillation Example')
ax.legend()
ax.grid(True, linestyle='--')

# 4. Show or Save
plt.show()
# fig.savefig('plot.pdf', dpi=300, bbox_inches='tight')

Critical Rules

✅ DO

• Use the OO interface (ax.method()) - It prevents errors in multi-plot scripts.
• Use bbox_inches='tight' - When saving, to ensure labels aren't cut off.
• Set dpi - Use 300+ for print, 72-100 for web.
• Close figures - Use plt.close('all') in loops to avoid memory leaks.
• Label everything - Every axis must have a label and units.
• Vector formats - Save as .pdf or .svg for academic papers (lossless scaling).
• Colorblind-friendly - Use tab10 or viridis colormaps.

❌ DON'T

• Mix plt. and ax. - It leads to "hidden state" bugs.
• Use plt.show() in loops - It blocks execution; use fig.savefig() instead.
• Manual legend placement - Let ax.legend(loc='best') try first.
• Hardcode font sizes - Use plt.rcParams.update({'font.size': 12}) for consistency.
• Use "Rainbow" (Jet) - It creates false gradients; use perceptually uniform maps like magma or inferno.

Anti-Patterns (NEVER)

# ❌ BAD: Mixing interfaces (State-based + OO)
plt.figure()
ax = plt.gca()
plt.plot(x, y) # Confusing state
ax.set_title('Test')

# ✅ GOOD: Consistent OO interface
fig, ax = plt.subplots()
ax.plot(x, y)
ax.set_title('Test')

# ❌ BAD: Overlapping subplots
fig, axs = plt.subplots(2, 2)
# Plots look squashed and titles overlap

# ✅ GOOD: Use constrained_layout or tight_layout
fig, axs = plt.subplots(2, 2, constrained_layout=True)

Anatomy of a Plot

Labels, Ticks, and Styles

fig, ax = plt.subplots()

ax.plot(x, y, 'o-', color='red', markersize=4, alpha=0.7)

# Explicitly setting limits
ax.set_xlim(0, 10)
ax.set_ylim(-1.5, 1.5)

# Controlling Ticks
ax.set_xticks([0, 2.5, 5, 7.5, 10])
ax.set_xticklabels(['Start', '1/4', 'Mid', '3/4', 'End'])

# Spines (Box around the plot)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)

# Adding text and arrows
ax.annotate('Local Max', xy=(1.5, 1), xytext=(3, 1.2),
             arrowprops=dict(facecolor='black', shrink=0.05))

Advanced Layouts

Subplots and GridSpec

# Simple 2x2 grid
fig, axs = plt.subplots(2, 2, figsize=(10, 10))
axs[0, 0].plot(x, y) # Top left
axs[1, 1].scatter(x, y) # Bottom right

# Complex grid (Uneven sizes)
fig = plt.figure(figsize=(10, 6))
gs = gridspec.GridSpec(2, 2, width_ratios=[2, 1], height_ratios=[1, 2])

ax1 = fig.add_subplot(gs[0, 0]) # Top left (large width)
ax2 = fig.add_subplot(gs[0, 1]) # Top right
ax3 = fig.add_subplot(gs[1, :]) # Bottom spanning all columns

Scientific Plot Types

Heatmaps and Colorbars

data = np.random.rand(10, 10)

fig, ax = plt.subplots()
im = ax.imshow(data, cmap='viridis', interpolation='nearest')

# Add colorbar
cbar = fig.colorbar(im, ax=ax, label='Intensity [a.u.]')

# Proper alignment of colorbar
from mpl_toolkits.axes_grid1 import make_axes_locatable
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.05)
fig.colorbar(im, cax=cax)

Histograms and Error Bars

# Histogram
data = np.random.normal(0, 1, 1000)
ax.hist(data, bins=30, density=True, alpha=0.6, color='g', edgecolor='black')

# Error bars
x = np.arange(10)
y = x**2
yerr = np.sqrt(y)
ax.errorbar(x, y, yerr=yerr, fmt='o', capsize=5, label='Data with noise')

3D Plotting

from mpl_toolkits.mplot3d import Axes3D

fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')

X = np.arange(-5, 5, 0.25)
Y = np.arange(-5, 5, 0.25)
X, Y = np.meshgrid(X, Y)
R = np.sqrt(X**2 + Y**2)
Z = np.sin(R)

surf = ax.plot_surface(X, Y, Z, cmap='coolwarm', linewidth=0, antialiased=False)
fig.colorbar(surf, shrink=0.5, aspect=5)

Formatting for Publication

Using LaTeX and RcParams

# Global styling
plt.style.use('seaborn-v0_8-paper') # or 'ggplot', 'bmh'

# LaTeX for labels
plt.rcParams.update({
    "text.usetex": True,
    "font.family": "serif",
    "font.serif": ["Computer Modern Roman"],
    "axes.labelsize": 14,
})

fig, ax = plt.subplots()
ax.plot(x, y)
ax.set_xlabel(r'$\alpha_{i} + \beta \sin(\omega t)$') # LaTeX string

Practical Workflows

1. Multi-dataset Comparison Workflow

def plot_comparison(datasets, labels):
    fig, ax = plt.subplots(figsize=(10, 6))
    colors = plt.cm.viridis(np.linspace(0, 1, len(datasets)))
    
    for data, label, color in zip(datasets, labels, colors):
        ax.plot(data['x'], data['y'], label=label, color=color, lw=1.5)
        ax.fill_between(data['x'], data['y']-data['std'], data['y']+data['std'], 
                        alpha=0.2, color=color)
    
    ax.set_title('Experiment Results Comparison')
    ax.legend(frameon=False)
    return fig, ax

2. Monitoring Real-time Data (Interactive)

# Use this in a Jupyter environment or script
plt.ion() # Interactive mode on
fig, ax = plt.subplots()
line, = ax.plot([], [])

for i in range(100):
    new_data = np.random.rand(10)
    line.set_data(np.arange(len(new_data)), new_data)
    ax.relim()
    ax.autoscale_view()
    fig.canvas.draw()
    fig.canvas.flush_events()
    plt.pause(0.1)

3. Creating a Cluster Map / Correlation Matrix

import pandas as pd

df = pd.DataFrame(np.random.rand(10, 4), columns=['A', 'B', 'C', 'D'])
corr = df.corr()

fig, ax = plt.subplots()
im = ax.imshow(corr, cmap='RdBu_r', vmin=-1, vmax=1)
ax.set_xticks(np.arange(len(corr.columns)), labels=corr.columns)
ax.set_yticks(np.arange(len(corr.index)), labels=corr.index)

# Loop over data dimensions and create text annotations.
for i in range(len(corr.index)):
    for j in range(len(corr.columns)):
        text = ax.text(j, i, f"{corr.iloc[i, j]:.2f}",
                       ha="center", va="center", color="black")

Performance Optimization

Plotting Large Data

# 1. Use 'agg' backend for non-interactive rendering
import matplotlib
matplotlib.use('Agg')

# 2. Use PathCollection for scatter plots with many points
ax.scatter(x, y, s=1) # slow for 1M points

# 3. Use marker='' (none) and only lines for speed
ax.plot(x, y, marker=None)

# 4. Decimate data before plotting
ax.plot(x[::10], y[::10]) # Plot every 10th point

Common Pitfalls and Solutions

Date/Time Axis issues

# ❌ Problem: Dates look like a black blob
# ✅ Solution: Use AutoDateLocator and AutoDateFormatter
import matplotlib.dates as mdates

fig, ax = plt.subplots()
ax.plot(dates, values)
ax.xaxis.set_major_locator(mdates.MonthLocator())
ax.xaxis.set_major_formatter(mdates.DateFormatter('%Y-%m'))
fig.autofmt_xdate() # Rotates labels

Multiple Legends on one plot

# ❌ Problem: Calling ax.legend() twice replaces the first one
# ✅ Solution: Manually add the first artist back
fig, ax = plt.subplots()
line1, = ax.plot([1, 2], [1, 2], label='Line 1')
line2, = ax.plot([1, 2], [2, 1], label='Line 2')

first_legend = ax.legend(handles=[line1], loc='upper left')
ax.add_artist(first_legend) # Add back
ax.legend(handles=[line2], loc='lower right')

Image Saving Quality (Clipping)

# ❌ Problem: Legend or Axis title is cut off in the .png file
# ✅ Solution:
fig.savefig('output.png', bbox_inches='tight')

Best Practices

1. Always use the OO interface (fig, ax = plt.subplots()) for scripts and modules 2. Save figures with appropriate formats - Use PDF/SVG for publications, PNG for web 3. Set DPI appropriately - 300+ for print, 72-100 for screen 4. Use `bbox_inches='tight'` when saving to prevent clipping 5. Close figures in loops to prevent memory leaks 6. Use colorblind-friendly colormaps - Avoid 'jet', prefer 'viridis', 'plasma', 'inferno' 7. Label all axes with descriptive names and units 8. Use `constrained_layout=True` for subplots to prevent overlap 9. Configure global styles with plt.rcParams for consistency 10. Test plots at target resolution before finalizing