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Robyn Woudstra edited this page Jan 2, 2026 · 6 revisions

Expression

Please note:
Expression heat maps use WebAssembly, which may take a few seconds to load completely. Once loaded, Heatmapper2 will run locally in your browser! This eliminates problems like server congestion and lag spikes, and file upload is much faster as you simply fetch from disk. Once the WebAssembly application is loaded, you can even work offline!
(An internet connection is required to load example files)

If you are using a browser that does not support WebAssembly (e.g. Internet Explorer or Opera Mini), you can check out Expression heat maps on the server.

Thanks to YeaJin Ko for preparing this Expression video tutorial:

Expression video tutorial

3D

Thanks to YeaJin Ko for preparing this 3D heat map video tutorial:

3D video tutorial

Pairwise

Please note:
Pairwise heat maps use WebAssembly, which may take a few seconds to load completely. Once loaded, Heatmapper2 will run locally in your browser! This eliminates problems like server congestion and lag spikes, and file upload is much faster as you simply fetch from disk. Once the WebAssembly application is loaded, you can even work offline!
(An internet connection is required to load example files)

If you are using a browser that does not support WebAssembly (e.g. Internet Explorer or Opera Mini), you can check out Pairwise heat maps on the server.

Welcome

  1. Once the application is loaded, you will see a settings sidebar on the left side of the screen, and three tabs in the main area. The first tab is the 'Welcome' tab, which provides introductory information about Pairwise heat maps and compatible file formats.

Heatmap

  1. To generate a heat map, select an example file or upload your own data using the file selector at the top of the sidebar.
  2. Then, navigate to the Heatmap tab. You should see your heat map in the centre of the screen. If you see an error message (e.g. "No data to display!"), please check the formatting of your input data. More information about Pairwise file formats can be found in the Format section of this wiki. If an example file fails to load, please check your internet connection. If you have a large dataset, it is recommended to toggle "Auto Update" off. If your dataset is small, you can leave "Auto Update" turned on, and see the results of setting changes almost instantly.
Pairwise-Walkthrough-01

  1. Pairwise heat maps can visualize either the distance or correlation between points. To toggle between these values, select either "Distance" or "Correlation" from the "Matrix Type" dropdown in the sidebar. If your input data contains zeros along the diagonal, it is assumed that this data is a pre-computed matrix. If "Distance" is selected, you can change the distance metric used via the "Distance Method" dropdown. If "Correlation" is selected, correlation methods are available instead.

  2. To make values appear smoother, you can apply an interpolation method to the heat map image. Selecting "None" displays the values with no interpolation.

  3. If your input data is a PDB file, you can specify which chain in the PDB you would like to visualize.

  4. If your input data is a FASTA file, you can specify the length of K-mer to use.

Pairwise-Walkthrough-02

Further settings and download options can be viewed by scrolling down in the sidebar. User settings can be downloaded as a .txt, .csv, .tsv, or .xlsx file for future reference.
Find out more about settings in the Interface section of this wiki.

Table

  1. To view the data itself, navigate to the "Table" tab. Here you can view the input data, download the input data, and even modify values, with changes reflected in the visualized heat map.

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