waldronlab / waldronlab/bugSigSimple
createTaxonTable - wide vs. narrow form
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- Dominant language
- R
- Stars
- 4
- Forks
- 18
- PR merge metrics
- No merged PRs in 30d
Description
Right now, createTaxonTable() outputs a very wide tibble with the entire taxonomy of the taxon presented as columns 7-13. This has some issues:
- It does not support domain which was added to the taxonomy so all the taxonomy is currently wrong
- It includes a column called "n_signatures" which I'm not sure what this means
- It also includes the metaphan name which feels unnecessary
Changes to this function should include:
- Remove n_signatures if it's not displaying anything useful
- Add an argument like "format = 'Full'/'Simple' " where full displays the full taxonomy columns and metaphlan name while simple only displays columns 1-6 and "Simple" is the default for that argument
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the createTaxonTable() entry point and inspect how its current columns are assembled, including the taxonomy, n_signatures, and metaphlan name. Check how domain is represented in the taxonomy before deciding the table shapes. Done means the default Simple format returns columns 1–6, while Full includes the requested taxonomy columns and metaphlan name, with n_signatures resolved as specified.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100