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Center normal node#177

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dan-knight merged 1 commit intomainfrom
hwinata-fix-normal-node
Apr 25, 2025
Merged

Center normal node#177
dan-knight merged 1 commit intomainfrom
hwinata-fix-normal-node

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@whelena
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@whelena whelena commented Apr 13, 2025

Description

Added a correction term to make sure normal node is centered when plotting.direction is left or right

Closes #176

Results

Screenshot 2025-04-12 at 22 25 30

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 requested a review from dan-knight April 13, 2025 05:28
@dan-knight
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Positioning looks good. I wonder if we should also rotate it? This is more of a scientific question than a software one. My thinking is to rotate the box, and the "N" as close to upright as possible? Or only rotate the box?

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whelena commented Apr 16, 2025

I think it makes the most sense for the "N" to remain upright, so its consistent with the orientation of the other node labels. As for the box, I'm not entirely sure—it could stay upright as well. Having an upright "N" inside a slightly rotated box (when plotting.direction = pi/8) might look disturbing.

These look ok I think, with the N + box upright
Screenshot 2025-04-15 at 18 30 50

@dan-knight dan-knight merged commit 5ae2d8c into main Apr 25, 2025
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@dan-knight dan-knight deleted the hwinata-fix-normal-node branch April 25, 2025 20:56
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Misaligned normal node when ploting.direction != 'down'

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