Skip to content
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

[FEAT] Fix, Implement PspA Figure #90

Open
falquaddoomi opened this issue Oct 9, 2024 · 0 comments · May be fixed by #93
Open

[FEAT] Fix, Implement PspA Figure #90

falquaddoomi opened this issue Oct 9, 2024 · 0 comments · May be fixed by #93
Labels
coding Coding experience (of any sort) would be helpful dataviz Data visualization enhancement New feature or request outreachy for outreachy interns package R package dev

Comments

@falquaddoomi
Copy link
Contributor

falquaddoomi commented Oct 9, 2024

We need to add figure 4 from the PspA paper, https://journals.asm.org/doi/epub/10.1128/msystems.00847-23. Similar to #88, we have some code, written when the paper was published, that was used to generate those figures, but it's likely out of date and wasn't written to use MolEvolvR's job outputs. The figure will need to be integrated into the MolEvolvR web app, both for displaying on the site and including in the downloadable report.

Any progress on the following tasks would be appreciated:

  • getting the figure to render with its original inputs
  • adapting the code to use MolEvolvR's job output

I've included a sample MolEvolvR job output, 5uNQ9l, to demonstrate what files are typically included in a MolEvolvR job.

5uNQ9l_full.tar.gz

See PR #93 for the current code. If you self-assign this issue also assign yourself to that PR. Once your PR is ready, you can convert it from a draft to a regular PR and request review. If you prefer to not use that PR as a starting point, you're also free to create your own.

@falquaddoomi falquaddoomi added enhancement New feature or request outreachy for outreachy interns package R package dev coding Coding experience (of any sort) would be helpful labels Oct 9, 2024
@falquaddoomi falquaddoomi linked a pull request Oct 9, 2024 that will close this issue
11 tasks
@falquaddoomi falquaddoomi added the dataviz Data visualization label Oct 9, 2024
Klangina pushed a commit to Klangina/MolEvolvR that referenced this issue Oct 22, 2024
 - Refactored  and merged R/tree.R CreateFA2Tree and ConvertFA2Tree.
- Parametrized every hardcoded value and path in ConvertFA2Tree
- Refactored convertAlignment2Trees to support running both modes.
- Backward compatible
- Updated all documentation for R/tree.R
Klangina added a commit to Klangina/MolEvolvR that referenced this issue Oct 22, 2024
 - Refactored  and merged R/tree.R CreateFA2Tree and ConvertFA2Tree.
- Parametrized every hardcoded value and path in ConvertFA2Tree
- Refactored convertAlignment2Trees to support running both modes.
- Backward compatible
- Updated all documentation for R/tree.R
@jananiravi jananiravi changed the title Fix, Implement PspA Figure 🆕 [FEAT] Fix, Implement PspA Figure Oct 26, 2024
@jananiravi jananiravi changed the title 🆕 [FEAT] Fix, Implement PspA Figure [FEAT] Fix, Implement PspA Figure Oct 26, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
coding Coding experience (of any sort) would be helpful dataviz Data visualization enhancement New feature or request outreachy for outreachy interns package R package dev
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant