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Kyle Kernick edited this page Apr 10, 2024 · 9 revisions

Heatmapper 2

Welcome to the Heatmapper Documentation! This documentation refers to Heatmapper 2. If you’re using the older, R-Based Heatmapper hosted at http://heatmapper.ca, you should looked here for relevant information.

If you’ve used the legacy Heatmapper, you may want to look at Running to see what’s new between versions, or if you want to better understand the core technologies used by the project. In summary, there are three ways to run Heatmapper:

  1. As a Web-Assembly, Client-Side application run in your browser, hosted at https://wishartlab.github.io/heatmapper2
  2. As a PyShiny, Server-Side application run in your browser, hosted at http://35.208.86.138
  3. As a Python application from your computer. See Running for details.

If your browser and system supports it, Heatmapper will run as a client-side, WASM application within your browser by default. Some applications, such as the Spatial Heatmapper, can only be run on the server, but Heatmapper will automatically switch the source based on the selected application and capabilities of the system.

Use the sidebar on the right to navigate through the documentation. For each heatmap, you can find general information about the heatmap is for, the input files that it supports, and a description of the settings and features that can be modified within the interface. For an outline of the interface, and an explanation of the various settings for each application, see Interface. For an outline of the support file formats each application supports, see Format.

Heatmap Overview

Heatmap Operating Mode Screenshot
Expression All Modes Displays unclustered (or previously clustered) data from transcriptomic (microarray or RNAseq), proteomic or metabolomic experiments.
Pairwise All Modes Displays two sub-classes of heatmaps: display all pairwise distances between the points in a data set or display correlations between all pairs of variables in a data set.
Image All Modes Display a heatmap over any image.
Geomap All Modes Display a heatmap based on country, state, province etc. political boundaries.
Geocoordinate All Modes Display data on geospatial coordinates (latitude and longitude).
3D No WebAssembly Support Displays data or textures on a 3D, interactive model.
Spatial No WebAssembly Support Display spatial molecular data, and visualize various related metrics.

References

Thanks to the following libraries for making Heatmapper possible:

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