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Empress 0.3.0: Beta Release

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@fedarko fedarko released this 06 Aug 01:20
· 190 commits to master since this release
v0.3.0
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Learn about vigilant mode.

New features

  • Enhance Empress / Emperor integration: now, clicking on a biplot arrow in Emperor reveals the corresponding node in the tree in Empress. In addition, this highlights the samples in the Emperor plot where this feature is found.
  • Add the ability to collapse clades of the tree based on sample / feature metadata coloring. For the rectangular and circular layouts two algorithms are supported ("symmetric" and "asymmetric"). For the unrooted layout only the asymmetric mode is supported. Users can select their algorithm of choice in the "Tree Properties" tab.

ccollapsing

  • Add an option to export the styled tree as an SVG file. This option can be found under the "Export" tab.
  • Add the ability to draw barplots that align with the tips of the tree (currently only supported for the rectangular layout). This feature allows users to visualize sample and feature metadata as tip-level annotations.

barplots-fancy-2

  • Improve line-width setting to be dependent on the number of leaves of the tree being displayed. The input is now relabeled to correctly reflect that this is "added" width as opposed to a scaling factor.
  • Add two new settings to ignore absent tips when propagating sample metadata coloring, and to prevent the camera to refocus when a node is selected (via Emperor the search bar). These options can be found in the "Tree Properties" tab.

Documentation

  • Improve installation documentation, and setup requirements to install latest Emperor development version.
  • Add a comprehensive tutorial that demonstrates many of the features available in Empress.
  • Rebrand integrated Empress+Emperor plots as Empire plots.

Bug fixes

  • Fix bug that would allow users to enter negative line-widths. All numeric inputs are now validated consistently.
  • Various bug fixes

Performance improvements

  • Stored tree data in a more efficient way in the visualization (#258).

Development enhancements

  • Create a utility script for front-end development, tests/python/make-dev-page.py. This script creates a standalone HTML document that can be used to update and modify the JS libraries without having to rebuild the page (#257).
  • Add support to preview built artifacts based on open pull requests. Links to the Q2-View URLs are posted in a comment by @emperor-helper.
  • Refactored various parts of the code to support direct testing (#187).
  • Add more comprehensive tests, applied consistent styling for tests, and updated to the latest version of QUnit.
  • Miscellaneous code and development documentation improvements.

Miscellaneous

  • Previously, sample metadata groups with no unique tips were removed from the legend shown during sample metadata coloring, and were not assigned colors from a color map. To make sample metadata barplots use consistent colors as the sample metadata coloring functionality, these groups are now assigned colors and preserved in the legend.

🌳 📊 💥

Acknowledgements

This work is supported by IBM Research AI through the AI Horizons Network. For more information visit the IBM AI Horizons Network website.

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