Publications

---

Change log

Version 0.8.4.0 (2021-03-18)

• Fix layer mapping of custom tree upload.
• Fix potential security vulnerabilities.
• Update author info.

Version 0.8.3.0 (2019-05-08)

• Update citation.
• Upgrade dependencies.

Version 0.8.2.0 (2019-03-13)

• Performance improvement
  • Loading of the viewer is reduced from 10 seconds to 2.5 seconds on average (4 fold speedup).
  • Visualization of the BRITE hierarchy at KO level does not crash the browser anymore (still not fast though).
• Addition of mapping to a color gradient when submitting to iPath.
• Addition of mapping values to circle area. The default is still to radius.
• Simplification of tooltip text: removal of duplicated names and hierarchy information.
• Fix of the search match highlight in Firefox.
• UX improvement: the size of highlighted nodes on mouseover is reduced to avoid hiding neighboring nodes.

Version 0.8.1.0 (2019-03-08)

• Enhancement of the search box for map elements.
• Addition of a cutoff slider for filtering the data submitted to iPath.
• Handling of matrices with duplicated entries by taking the sum of duplicates.
• Handling of matrices that result in no mapping to the hierarchy.

Version 0.8.0.0 (2019-02-28)

• Improvement of iPath integration
  • Addition of control for color, width, opacity, and global map selection.
  • Default Functree 2 color palette is used for the first submission.
  • Streamlining of the controls layout and the UI.
  • Bug fix: selection of leaf nodes with value > 0 only.
• Addition of bar plots to "Module undefined" nodes to highlight the amount of pathway KO not assigned to a module.

Version 0.7.6.3 (2019-02-25)

• Addition of an annotation section to the TSV reference tree format.

Version 0.7.6.2 (2019-02-15)

• Addition of a toggle action to show/hide node labels.
• Addition of a description to the database selection.
• Upgrade of Flask.

Version 0.7.6.1 (2019-01-18)

• Addition of a help section on the Functree explorer page, and improvement of the main documentation.

Version 0.7.6 (2019-01-15)

• Addition of a zoom control widget.
• Replacement of D3 categorical20 color palette by the color blind friendly palette tableau10.

Version 0.7.5 (2018-08-10)

• Addition of an option to divide ortholog abundance by its incidence on each layer.

Version 0.7.4 (2018-06-20)

• Performance improvement: mapping time is reduced to around 15 seconds on dev machine using the example profile.tsv.

Version 0.7.3 (2018-06-19)

• Performance improvement: mapping time is reduced from 3 minutes to 1 minute and 20 seconds. Module coverage computation time is lowered from 80 seconds to 5 seconds.