Online heatmap maker, no signup

Free Heatmap Generator for Excel, CSV, and Data Matrices

With this Heatmap Generator, paste a labeled matrix from Excel or upload a CSV/TSV file. Normalize rows or columns, cluster similar patterns, check missing values and export SVG, PNG or an ordered CSV. No code, no account and no watermark.

Paste from Excel or upload CSV/TSVRow and column Z-scoresHierarchical clustering with dendrogramsData stays in your browser

Enter a Matrix and Choose Heatmap Settings

Put row names in the first column and column names across the first row. Blank, NA, NaN, null and “-” cells count as missing.

Paste a labeled numeric matrix

Copy cells straight from Excel or Google Sheets, or paste comma-, tab- or semicolon-separated text.

gene-expression.csv

Chart title

Normalization

Color palette

Hierarchical clustering

Distance metric

Show cell valuesShow dendrograms

The matrix looks valid. Confirm the normalization, clustering and color scale before you publish or share the figure.

Your matrix is parsed, transformed, clustered and rendered in your browser. It is never uploaded.

Live heatmap and method summary

8
Rows: 6
Columns: 0
Missing: -1.19–1.26
Range

Normalization: row-z · Hierarchical clustering: both · Distance metric: correlation

Z-scores use the population standard deviation. Clustering uses average linkage with the selected Euclidean or correlation distance.

Heatmap basics

What a Heatmap Shows

A heatmap is a color-coded grid for a numeric matrix. Rows and columns stay as separate categories, and the color scale shows high, low, similar and unusual values without reading every number. Researchers use heatmaps for gene expression, correlation, model errors, activity and business data.

Sequential palettes suit values that rise from low to high. Diverging palettes suit values around a meaningful midpoint, such as zero, change from baseline or a Z-score. The legend is part of the evidence, so it must say what the colors mean.

Clustering can reorder rows or columns so similar profiles sit together. A dendrogram records that order, but it does not prove biological or causal groups. Read clusters alongside the study design and the source data.

Matrix

Rows and columns define the observations or variables being compared.

Color scale

A legend maps numeric values to color and identifies the midpoint.

Normalization

Row or column Z-scores change the question from magnitude to relative pattern.

Clustering

A distance metric and a linkage rule decide which similar profiles sit together.

Methods and references

Make Heatmap Scaling and Clustering Reproducible

A heatmap can change a lot with scaling, distance, linkage and color limits. Record each choice in the figure caption or methods section.

Reference documentation reviewed: September 2026

ReferenceTopicWhat to verifyDocumentation

Reference

SciPy

Topic

Hierarchical clustering

What to verify

Verify the distance metric, average-linkage method, and leaf order used for the dendrogram.

Documentation

linkage

Reference

R stats

Topic

Scaling

What to verify

State whether values were centered and scaled by row or column before plotting.

Documentation

scale

Reference

Matplotlib

Topic

Color mapping

What to verify

Choose a sequential or diverging colormap that matches the numeric meaning and remains legible.

Documentation

colormaps

Method labels help reproducibility but do not replace checking the figure against your analysis code or source matrix.

Heatmap Examples for Research and Data Analysis

Load any example to inspect its raw matrix, normalization, clustering order, missing values and color scale, then edit it.

Built for real matrices

Heatmaps for Gene Expression, Correlation, and Excel Data

One workflow that keeps every step visible, from exploration and teaching to reporting and figure preparation.

Researcher reviewing a clustered gene expression heatmap

Biomedical and omics researchers

Compare genes, proteins, metabolites, samples, and treatment conditions with row scaling and clustering.

Data scientist inspecting a correlation matrix heatmap

Statisticians and data scientists

Visualize correlation matrices, confusion matrices, and multivariate features without hiding numeric values.

Analyst creating a heatmap from Excel data

Excel and CSV analysts

Move directly from a spreadsheet matrix to an ordered, shareable visual and exportable data table.

What the generator does

Heatmap Features for Excel, CSV and Clustering

Turn a labeled matrix into a chart you can audit, with every transformation kept visible.

Turn an Excel or CSV Matrix into a Heatmap

Paste spreadsheet cells or upload a file and get a labeled heatmap without reshaping a clean matrix. Missing cells stay visible, and unexpected text is flagged before you export.

Try it with your data

Heatmap Generator importing an Excel and CSV matrix

Reveal Patterns with Scaling and Dendrograms

Compare relative profiles with row or column Z-scores, then group similar rows or columns with Euclidean or correlation distance and a visible dendrogram.

Try it with your data

Heatmap clustering controls with row and column dendrograms

Edit a Publication-Ready SVG without a Watermark

Download an editable SVG for manuscript layout, a high-resolution PNG for slides, and an ordered CSV that keeps the displayed row and column order.

Try it with your data

Heatmap export options for SVG PNG and ordered CSV

Method guardrails

How Normalization and Clustering Change a Heatmap

The same matrix can tell a different story after scaling or reordering. The generator names each choice so reviewers can reproduce it.

Raw values

Preserve magnitude and units when every row and column is directly comparable.

Row Z-score

Center and scale each row to compare relative patterns rather than absolute magnitude.

Distance

Euclidean distance compares magnitude; correlation distance emphasizes profile shape.

Average linkage

Clusters merge according to the average pairwise distance between their members.

Heatmap normalization and hierarchical clustering method guide — Scaling changes values; clustering changes order. Neither step creates new observations.Methods visible

Four steps

How to Create a Heatmap from Excel or CSV

Go from a spreadsheet matrix to a labeled, exportable heatmap in four steps.

Paste or upload the matrix

Place column labels in the first row and row labels in the first column.

Check missing values

Review cells parsed as missing and fix any unexpected text.

Choose scale and clustering

Select normalization, palette, distance, and which dimensions to reorder.

Export chart and data

Download SVG or PNG plus an ordered CSV that matches the displayed heatmap.

Make your heatmap

Four steps for creating a heatmap from Excel or CSV — Keep the source matrix and method settings with the exported figure.

Continue the analysis

Related Research Visualization Tools

Pick another tool when your question involves effect sizes, distributions or evolutionary relationships.

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Forest Plot Maker

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Phylogenetic Tree Generator

Visualize evolutionary relationships when a distance matrix represents taxa.

Frequently asked questions

Heatmap Generator FAQ

How do I create a heatmap from Excel data?+

Copy a rectangular range in Excel and paste it into the Heatmap Generator. Put column labels in the first row and row labels in the first column. The tool reads tab-separated cells automatically, keeps blank or NA cells as missing values, and draws the heatmap as soon as the matrix is valid.

Can I upload a CSV or paste a labeled data matrix?+

Paste comma-, tab- or semicolon-separated data, or upload a CSV, TSV or TXT file. The first row supplies column labels and the first column supplies row labels. Blank, NA, NaN, null and dash cells stay visibly missing instead of being silently converted to zero.

What is the difference between sequential and diverging heatmap colors?+

Use a sequential palette such as Viridis or Cividis when values run from low to high on one scale. Use the diverging blue–white–red palette when values have a meaningful center, such as zero, change from baseline or a Z-score. Keep the colorbar visible when you report the result.

How do I make a correlation heatmap?+

Create a square matrix with the same variables across the first row and first column, then paste or upload it. Keep the raw correlation coefficients and choose the diverging palette so zero is the midpoint. Turn on cell values when readers need the exact coefficients next to the colors.

Should I normalize heatmap data by row or by column?+

Choose row Z-scores to compare each feature’s relative pattern across samples, and column Z-scores to compare patterns within each sample or condition. Keep raw values when all cells share comparable units and absolute size matters. Record the normalization in the figure caption or methods section.

Does the Heatmap Generator support clustering and dendrograms?+

Cluster rows, columns or both, then show dendrograms beside the reordered matrix. The tool uses average linkage with Euclidean distance for magnitude differences or correlation distance for profile shape. The chosen normalization, clustering dimensions and distance stay visible beside the chart for review.

How does the Heatmap Generator handle missing values and exports?+

Blank cells and common NA markers get a neutral missing-value color, and unexpected text is counted for review. Parsing, normalization, clustering and rendering all happen in your browser. Export an editable SVG, a high-resolution PNG or an ordered CSV with no account or watermark, and keep the source matrix with the figure.

Ready to plot your matrix?

Create Your Heatmap in the Browser

Paste a matrix, choose normalization and clustering, check the color scale and export the figure with its ordered data. No signup, no watermark.

Start plotting your matrix