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Hwinata fix text annotation #150

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@whelena whelena commented Oct 4, 2024

Description

Fixing 2 main issues:

  1. Text annotations are missing from plot.
  2. Test positioning assume radial edges, need to optionally adjust for when using 'dendrogram' mode

The first problem is due to a missing segment from the old (pre-plyr) version, where line 517-546 is missing

Closes #139

Checklist

  • This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
    Disclosing PHI is a major problem1 - Even a small leak can be costly2.

  • This PR does NOT contain germline genetic data3, RNA-Seq, DNA methylation, microbiome or other molecular data4.

  • This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

  • I have read the code review guidelines and the code review best practice on GitHub check-list.

  • I have set up or verified the main branch protection rule following the github standards before opening this pull request.

  • The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

  • I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

Footnotes

  1. UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records

  2. The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records.

  3. Genetic information is considered PHI.
    Forensic assays can identify patients with as few as 21 SNPs

  4. RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity.

@whelena whelena force-pushed the hwinata-fix-text-annotation branch from b0b6440 to 195ce67 Compare October 4, 2024 20:19
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whelena commented Oct 4, 2024

Fixed issue 1 by adding a for loop.

All the force pushed is because I messed up and branched off the danknight-scalebar branch instead of main. Should be good now!

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whelena commented Oct 4, 2024

Fixed issue 2 by considering mode when adding text. The fix improves readability in dendrogram mode without affecting `radial mode

Before

Screenshot 2024-10-04 at 4 01 11 PM

After

Screenshot 2024-10-04 at 4 01 55 PM

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