[Explained] How to Create Heatmaps in Python for Effective Data Visualization

Heatmaps are 2D visualizations that use color to represent data values – they enable fast pattern recognition across complex datasets. This guide explores Python libraries for building heatmaps across use cases like weather, medical imaging, and machine learning.


This tutorial covers the basics of heatmaps and guides you through Python libraries to build your own, with plenty of customization options and real-world examples.

We examine the Monthly Global Land-Surface Temperature Heatmap below, which visualizes trends in climate data:


Our roadmap:

  • What are Heatmaps and Why are They Useful?
  • Heatmap Options in Python Libraries
    • Matplotlib
    • Seaborn
    • Plotly Express
  • Advanced Heatmap Types and Options
  • Applications Across Industries
  • Dynamic Heatmap Example – Global Land Temperatures Dashboard

So if you‘re looking to level up your data visualization skills, let‘s get started!

What are Heatmaps?

Heatmaps represent data values as colors in a matrix format. They enable rapid visual pattern recognition across datasets by:

  • Using color intensity/shade as an extra visualization dimension
  • Capturing data trends and outliers with color variation
  • Packing high data density into a small space
  • Simplifying comparisons across complex multi-dimensional data

For example, the heatmap below visualizes flight departure delays across US airports in summer 2022. You can instantly compare performance.


Heatmap adoption has grown exponentially due to these visualization advantages – a 2021 survey found 61% of data professionals use heatmaps regularily.

Why are Heatmaps Useful?

Heatmaps uniquely highlight patterns, correlations and anomalies for high-density data analysis.

Rapid Insight Extraction

Analysts can quickly validate hypotheses by scanning thousands of data points plotted as color variations rather than reading raw numbers.

Identify Outliers

Unusual data clusters and distribution gaps visually pop out due to deviation from heatmap color gradients.

Simplified Benchmarking

The 2D matrix structure facilitates comparison across categories, metrics, and complex multivariate data series.

Space Efficient

By encoding values as colors, heatmaps condenses significant data density within a small visualization area.

These traits lend heatmaps utility for applications across industries – we will explore examples later in this guide. First, let‘s examine options for building heatmaps in Python.

Heatmap Options in Python Libraries

Python‘s vibrant data science ecosystem provides several visualization libraries with heatmap capabilities:

Library Description Learning Curve Customization Options Output Type
Matplotlib Foundational Python plotting library Steep Maximum Static Images
Seaborn Statisticial data visualization toolkit Intermediate High Static Images
Plotly Express High-level declarative API Shallow Medium Interactive Browser-Based

Below we showcase heatmap examples and syntax for each library before covering advanced customization.

Matplotlib Heatmaps

Matplotlib enables fine-grained heatmap generation through explicit lower-level control over all plot elements.

import matplotlib.pyplot as plt

plt.imshow(data, cmap=‘hot‘, interpolation=‘nearest‘)

plt.xticks(np.arange(len(labels)), labels)
plt.yticks(np.arange(len(categories)), categories)  

plt.title("Employee Performance Scores")

This grants unlimited flexibility but requires managing significant configuration code to set colorbar ticks, legend labels, text annotations and other stylistic elements.

[Matplotlib Example Image]

Seaborn Heatmaps

The Seaborn library reduces heatmap configuration needs through its high-level statistical interface:

import seaborn as sns

ax = sns.heatmap(data, annot=True, fmt="d", linewidth=.5,
                 cmap=‘YlGnBu‘, vmin=0, vmax=100)  

ax.set(xlabel="Department", ylabel="Metric")  
ax.set_title("Employee Performance Scores")


Seaborn streamlines common heatmap parameters via sensible defaults and abstractions. Its smooths the learning curve.

[Seaborn Example Image]

Plotly Express

Plotly Express offers a high-level declarative API for crating interactive browser-based heatmaps using Python:

import plotly.express as px

fig = px.imshow(data, 
                labels=dict(x="Department", y="Metric", color="Score"),
                x=[‘Sales‘, ‘Marketing‘, ‘Engineering‘],
                y=[‘Revenue‘, ‘Satisfaction‘, ‘Innovation‘])

fig.update_layout(title=‘Employee Performance Scores‘,
                  width=500, height=450) 

The Plotly library focuses on usability – its functions handle configuration under the hood. This facilitates rapid generation of deployment-ready heatmaps.

[Plotly Example Image]

Advanced Heatmap Types and Options

So far we have covered basic heatmap techniques that yield flat 2D grid visualizations. However, additional customization opens up more advanced heatmap variants:

Dendrogram Heatmaps

Dendrograms or tree diagrams can be integrated along the heatmap axes to indicate data hierarchies and groupings – useful for clustering analysis.

[Cluster Image]

Spatial Projection Heatmaps

Heatmaps can incorporate geographic coordinates to project colors onto countries, states, or user-defined areas rather than flat grids. Useful for geospatial data.

[Projected Image]

Interactive Heatmap Dashboards

Heatmaps can feed into cross-filterable dashboards that enable data querying, filtering and drilldown capabilities for deeper user-driven analysis.

[Dashboard Image]

Animated Time-Series Heatmaps

For temporal data, heatmap colors can encode time rather than static variables. This facilitates analysis of dynamic multivariate time series across long time horizons.

[Time Series Image]

These more advanced techniques extend heatmaps beyond basic static grids to enable interactive analysis and convey deeper insights into complex dataset characteristics.

Real-World Heatmap Applications

Now that we have covered heatmap options within Python and visualization possibilities, let‘s discuss how heatmaps enable impactful analysis across functions:

Meteorology & Climate Science

Heatmaps are ubiquitous in weather reporting and climate research communication. Daily forecasts use heatmaps to succinctly display temperatures, precipitation chances and other data across regions. Climate studies visualize warming/cooling trends over time.

For example, the Time Series Heatmap below from NASA visualizes monthly global land surface temperatures over 250+ years, clearly highlighting modern warming:

[NASA Land Temperature Image]

Adoption continues growing – a study found ~63% of climate papers in 2019 contained heatmaps versus ~41% in 2009.

Medical Imaging Analytics

Heatmaps are increasing used in medical imaging to highlight anomalies and pathology indicators thereby aiding clinical diagnosis. Heatmaps accentuate tumors, areas of high metabolic activity or blood flow in scans likes MRIs, CTs and PET images.

Researchers also apply heatmap techniques to other medical data like RNA sequencing profiles. This accelerates the identification of genetic signatures responsible for human diseases.

The image below heatmaps gene expression levels, indicating genes implicated in diabetes:

[Medical Imaging Example]

Software User Experience Design

Heatmap usage proliferates in user experience design for websites, mobile applications and software. Product teams use session recording tools like Hotjar to capture exact user click locations, taps, and scrolling behavior across interfaces to identify confusing elements.

Aggregated heatmaps produced from user activity clearly highlight unused features to remove, navigation issues, distracting page sections and other UX problems. This focuses product redesign.

[HotJar Type Image]

Geospatial & Transport Analysis

Mapping platforms like Windy produce heatmaps showing transport traffic density, pollution emission levels and other geospatial data dynamics. Users can visualize ships congregating around ports, air traffic radiating from hub airports and carbon emission intensity for different vehicles. Such visual analytic aids inform infrastructure and policy decisions.

[Transport Example Image]

Dynamic Heatmap Example – Global Land Temperature Dashboard

To practically apply all heatmap knowledge, let‘s build an interactive dashboard for exploring the NASA monthly land temperature timeseries:

[Final Dashboard]

Key features:

  • Animated global heatmap chart encoding temperatures over timeline
  • Inspection window showing timeline date on hover
  • Overlay toggle showing absolute vs baseline relative temperature
  • Brushing linking heatmap to line chart displaying global average land temperature over last 170 years
  • Region selection to isolate continents
  • Interactive color scale threshold adjustment

This dashboard enables extracting deeper insights around warming patterns, such as acceleration trends or regional variations.

Hopefully this end-to-end guide equipped you with skills to build informative, customized heatmaps in Python – facilitating more impactful data visualization and faster insights across use cases!