Support ignoring branch lengths during layout #271
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In addition, by moving the layout calculation to javascript, it would help simplify the python code. In particular #155 Also, I believe that we would also get a slight performance boost since layouts require looping through the tree which python is not very efficient at. |
fedarko
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Aug 13, 2020
related to biocore#271, but needs extending to other layouts
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fedarko
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Aug 26, 2020
* rectangular * max height * finished layout * STY: Add style * TST: Add tests * DOC: Update documentation * added unrooted * added console * ENH: Remove print statement * ENH: first draft of JS circular layout! * MNT: remove max_clradius from python circ layout (wasn't getting used anywhere. why was i keeping track of this lol) * STY: prettify * STY: jshint and prettier fixes * DOC: add note about root and repositioning * TST: port one of the circ layout test cases to js * TST: support+test circ layout for 1-child nodes Progress on #184. Since it looks like the unrooted layout handles these properly, all that's left for this issue should be just not drawing arcs for internal nodes with 1 child. Should be doable by modifying the js circular layout to give 1-child nodes -1 for their arc / angle values or something to signal to empress.js to not bother with arcs. * ENH: parameterize circular layout a bit related to #271, but needs extending to other layouts * PERF: rip out JS rect/circ layout scaling code I was having precision issues with the circular layout scaling (tldr: Math.cos(Math.PI / 2) is very close to but not quite 0, so it was messing up the max / min X computation), but this makes it so we shouldn't have to even worry about things for this case. * MNT: rip out now-unused scaling code in layouts * DOC: add tmp note abt vertical lines & rect layout * DOC: add note about root shifting and xr * TST: unbreak rect layout tests & port some docs * TST: unbreak bit of the c. layout tests * perf boost * TST: unbreak vert. straight-line circ layout test Close to making sure #184 is done :) * TST: unbreak another circ layout test Gonna say that this closes #184. * TST: finish unbreaking circ layout tests :3 Closes #184! I forget if i already did that so i'm doing it again. * TST: test no-root-length case in circ layout * TST: Add branch length preservation test The JS circular layout is now officially fully tested! Nice. * STY: prettify * TST: Add ignoreLengths test * TST: Test > 2pi start angle and ignoreLengths Verifies that big start angles don't break things, and that the two params play nicely * code before removing interations * finsished unrooted * removed names (need tests) * need to verify tests * removed coords * checkpoint before opt _proj * ENH: Remove layouts from Python All layout code is now implemented in JavaScript so we no longer need this here. ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▓▓▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒░░▒▒░░▒▒░░▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▓▓▒▒░░▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒ ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒░░░░▒▒░░▒▒░░▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒ 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stylechecks * replaced all _nameToKeys * fixed tests * finished tests * finished tests * prettified * style * Apply suggestions from code review Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Marcus Fedarko <[email protected]> * linted * Apply suggestions from code review Co-authored-by: Marcus Fedarko <[email protected]> * compute layout on demand * addressed comments * error in .travis.yml * fixed test * pinned prettier to 2.0.5 * test * print * addressed comments * address comments Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Marcus Fedarko <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Marcus Fedarko <[email protected]>
fedarko
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Sep 1, 2020
Closes biocore#271. pretty sure clade collapsing breaks here slightly -- gotta fix
ElDeveloper
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Sep 2, 2020
… panel UI; some minor clade collapsing changes (#363) * ENH: polish up "tree properties" UI in side panel * ENH: add ignoreLengths params for all layout funcs * ENH: polish tree properties ui more * ENH: improve 'focus on selected nodes' docs * ENH: add prototype of dynamic ignore-lengths! :) Closes #271. pretty sure clade collapsing breaks here slightly -- gotta fix * MNT: ignoreLen fixes; color clade root (fix #321) * DOC/BUG: rm collapsed clade caching+update cc docs There was stuff about how DEFAULT_COLOR nodes would get ignored, and now that should be fixed (?) * MNT: simplify ignoreLengths layout code also add a note about root length in unrooted layout (?) * MNT: reorder layout func docs re ignoreLengths * STY/MNT: simplify ignoreLengths use in bp tree * TST: unbreak layout tests * TST: test ignoreLengths in rect layout * ENH: 'node lengths' -> 'branch lengths' in UI Thanks @ElDeveloper * TST: add getTotalLength ignoreLengths tests
fedarko
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Nov 5, 2020
* rectangular * max height * finished layout * STY: Add style * TST: Add tests * DOC: Update documentation * added unrooted * added console * ENH: Remove print statement * ENH: first draft of JS circular layout! * MNT: remove max_clradius from python circ layout (wasn't getting used anywhere. why was i keeping track of this lol) * STY: prettify * STY: jshint and prettier fixes * DOC: add note about root and repositioning * TST: port one of the circ layout test cases to js * TST: support+test circ layout for 1-child nodes Progress on #184. Since it looks like the unrooted layout handles these properly, all that's left for this issue should be just not drawing arcs for internal nodes with 1 child. Should be doable by modifying the js circular layout to give 1-child nodes -1 for their arc / angle values or something to signal to empress.js to not bother with arcs. * ENH: parameterize circular layout a bit related to #271, but needs extending to other layouts * PERF: rip out JS rect/circ layout scaling code I was having precision issues with the circular layout scaling (tldr: Math.cos(Math.PI / 2) is very close to but not quite 0, so it was messing up the max / min X computation), but this makes it so we shouldn't have to even worry about things for this case. * MNT: rip out now-unused scaling code in layouts * DOC: add tmp note abt vertical lines & rect layout * DOC: add note about root shifting and xr * TST: unbreak rect layout tests & port some docs * TST: unbreak bit of the c. layout tests * perf boost * TST: unbreak vert. straight-line circ layout test Close to making sure #184 is done :) * TST: unbreak another circ layout test Gonna say that this closes #184. * TST: finish unbreaking circ layout tests :3 Closes #184! I forget if i already did that so i'm doing it again. * TST: test no-root-length case in circ layout * TST: Add branch length preservation test The JS circular layout is now officially fully tested! Nice. * STY: prettify * TST: Add ignoreLengths test * TST: Test > 2pi start angle and ignoreLengths Verifies that big start angles don't break things, and that the two params play nicely * code before removing interations * finsished unrooted * removed names (need tests) * need to verify tests * removed coords * checkpoint before opt _proj * ENH: Remove layouts from Python All layout code is now implemented in JavaScript so we no longer need this here. ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▓▓▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒░░▒▒░░▒▒░░▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▓▓▒▒░░▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒ ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒░░░░▒▒░░▒▒░░▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░▒▒▒▒▒▒▒▒▒▒ 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stylechecks * replaced all _nameToKeys * fixed tests * finished tests * finished tests * prettified * style * Apply suggestions from code review Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Marcus Fedarko <[email protected]> * linted * Apply suggestions from code review Co-authored-by: Marcus Fedarko <[email protected]> * compute layout on demand * addressed comments * error in .travis.yml * fixed test * pinned prettier to 2.0.5 * switch to index buffers * compress rgb * addressed comments * checkpoint * check point * fixed all buffers? * added console.log * checkpoint * merged with master * finished tests * removed unused function * addressed @fedarko comments * Apply suggestions from code review Co-authored-by: Marcus Fedarko <[email protected]> * addressed @fedarko's comments * fixed style * fixed export svg tree * fixed collapse clade issue * Apply suggestions from code review Co-authored-by: Marcus Fedarko <[email protected]> * addressed @fedarko's comments * changed default color * addressed @fedarko's comments Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Marcus Fedarko <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Marcus Fedarko <[email protected]>
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Suggestion from @gibsramen last week.
This (along with #170) would be a nice use case of doing layouts in the JavaScript code (#213), since that'd allow users to compare the same tree with and without branch lengths being used quickly.
For reference, here are some comparison screenshots on the moving pictures dataset (coloring by phylum):
Unrooted
With branch lengths
Uniform branch length of 1
Rectangular
With branch lengths
Uniform branch length of 1
Circular
With branch lengths
Uniform branch length of 1
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