How to Make Heatmap

Heatmaps show patterns across many rows and columns, especially when values are easier to compare by color than by exact numbers.

Prepare the matrix

Use rows for genes, proteins, samples, or features and columns for conditions or samples. Add metadata columns separately.

Choose the scale

Use a diverging palette for values centered around zero and a sequential palette for values that only increase.

Add annotations

Sample groups, treatment status, batch, and cluster labels help readers understand patterns without reading every row label.

Common mistakes

Do not overload the figure with unreadable labels. Use selected row labels or a supplement when the matrix is very large.

Try it in SciFigure AI

Open the Heatmap Generator, upload a matrix, and request clustering plus annotation bars.