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Phylocanvas as a BioJS component for the Galaxy charts #3850

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merged 8 commits into from Apr 4, 2017

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@anuprulez
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commented Mar 30, 2017

Introduction:

This PR introduces Phylocanvas as a BioJS component for the Galaxy charts to visualize phylogenetic/ evolutionary trees which themselves are pivotal to understand ancestral relationships among innumerable species of life forms. Phylocanvas offers an interactive view of the phylogenetic trees.

First look:

1

2

From this library, we include the following features:

  • Choose among five different tree types - Circular, Diagonal, Hierarchical, Radial and Rectangular.
  • Select different colors for trees, highlighted and selected sections of a tree.
  • Collapse and prune part(s) of a tree.
  • Show/hide and align labels of the leaves of a tree.
  • Select different shapes of leaves of a tree.

Collapsed part is dark shaded:

3

Circular tree type:

4

Data format:

The text files containing data in Newick (tree) notation can be used to visualize the trees. Few data files to go through the features:

file1.txt
file2.txt
file3.txt
file4.txt
file5.txt
file7.txt

Courtesy:

Phylocanvas is maintained by Centre for Genomic Pathogen Surveillance (CGPS)

Credits:

Thanks a lot to Aysam Guerler (@guerler) and Björn Grüning (@bgruening) for their suggestions and review.

Note:

While reviewing, we found a missing feature in the library (for Radial tree type) and opened a feature request here.

All suggestions are welcome. Thanks a lot!

@bgruening

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commented Mar 30, 2017

It's getting better and better :)
Thanks a lot @anuprulez!

@galaxybot galaxybot added the triage label Mar 30, 2017

@galaxybot galaxybot added this to the 17.05 milestone Mar 30, 2017

return {
title : 'Phylogenetic Tree Visualization',
library : 'BioJS',
datatypes : [ 'txt', 'nwk' ],

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@nsoranzo

nsoranzo Mar 30, 2017

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If these are Galaxy datatypes, then the only correct one is nhx.

@gregvonkuster

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commented Mar 31, 2017

@anuprulez Wow! This is awesome! Thanks so much for this - this will be so beneficial some of what I'm involved in! ;)

@bgruening

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commented Mar 31, 2017

@nsoranzo is this ok now?

@nsoranzo

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commented Mar 31, 2017

Yes, thanks.

@anuprulez

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commented Apr 3, 2017

@bgruening @guerler I merged this branch with the dev, can this PR be merged? Thanks!

@guerler

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commented Apr 4, 2017

Can you rebase/undo the merge and make one clean merge? I am not sure how to check if this merge is ok and would like to avoid a bad merge since those are very difficult to resolve down the road.

@anuprulez anuprulez force-pushed the bgruening:phylocanvas branch from 4ef2aa5 to 0c3f798 Apr 4, 2017

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commented Apr 4, 2017

@guerler I reverted the last two commits and did one clean merge with dev.

@guerler guerler merged commit 6f4e242 into galaxyproject:dev Apr 4, 2017

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@anuprulez anuprulez deleted the bgruening:phylocanvas branch Apr 4, 2017

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commented Apr 4, 2017

@guerler Thanks a lot for merging :)

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