New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Project 9: Using CollapseTree with Taxonomic Metadata #9

abaghela opened this Issue Aug 2, 2017 · 4 comments


None yet
3 participants

abaghela commented Aug 2, 2017

Large phylogenetic trees with hundreds or even thousands of nodes are impractical to view, and those who need them in their research have limited options for manipulating trees of this size. The collapseTree function in R's phytools package allows users to manually select branches of a phylogenetic tree to collapse, which achieves what the viewer of a large tree might want, but manually selecting the branches becomes difficult for the largest trees, or if the user would like to quickly make a series of different views of the same large input tree. By using taxonomic rank metadata and a stylesheet indicating which taxa should be collapsed, the existing collapseTree function could be used to be used to automate how branches in the tree are collapsed.

For collapseTree, the team will work towards adding the following functionalities:

  1. Collapse a specific set of tree tips, info supplied as a separate metadata object in the form of a stylesheet.

  2. Collapse a specific set of taxa to a specific taxonomic level, info supplied as taxonomy strings for each tree tip in metadata, plus a stylesheet that designates the desired level of detail for specific taxonomic groups.

Team Lead: Evan | | @morien | | UBC Botany

@abaghela abaghela changed the title from Project 9: to Project 9: Using CollapseTree with Taxonomic Metadata Sep 8, 2017


This comment has been minimized.


oganm commented Sep 19, 2017

it doesn't seem like it's possible to pick this project as a choice in the application. Is it full already?


This comment has been minimized.


abaghela commented Sep 19, 2017

Sorry about that, we will fix this. If you are interested in this project I will take note.



This comment has been minimized.

jakelever commented Oct 10, 2017

Hey team lead, we've been gathering Github IDs for your team members. As you've likely been notified, we've created a project repo for you that you are now the admin of and have added the team members to this. We've received almost everyone's Github ID and will continue to add members as we got their Github IDs.

Project repo:

Feel free to rename the repo as appropriate. Note that the repo currently has an MIT license. Amend this as required. It'd be a great idea to start a discussion on this repo with information to get your team members started (e.g. some small suggested reading, things to look up, etc). We will also be adding everyone to Slack and creating a specific channel for each project. This may be an easier way to communicate.

Thanks, Jake
obo the Hackseq organising committee


This comment has been minimized.


oganm commented Oct 11, 2017

I am afraid I won't be able to join this year. Sorry for the inconvenience

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment