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Node-by-node control of node rendering ("nodeless" mode) #132

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merged 14 commits into from
Aug 6, 2024

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dan-knight
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@dan-knight dan-knight commented Jul 19, 2024

Description

Allows node-by-node control of node ellipse drawing with a draw.nodes column in the tree input data frame. This was previously handled globally with an argument of the same name on SRCGrob. Also includes unit-tests and new examples in the package manual and User Guide vignette.

Example

nodeless <- data.frame(
    parent = c(
        NA, 1, 2, 2, 2, 
        3, 3, 3, 
        4, 4, 4, 4, 4, 
        5, 5, 5, 5
        ),
    draw.node = TRUE,
    spread = NA
    );
nodeless$spread[6:nrow(nodeless)] <- 0.6;
nodeless$draw.node[c(2, 6:nrow(nodeless))] <- FALSE;

grid.draw(SRCGrob(nodeless));
Screenshot 2024-08-02 at 12 13 55 PM

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.

@dan-knight dan-knight added the enhancement New feature or request label Jul 19, 2024
@dan-knight dan-knight requested a review from whelena July 19, 2024 23:04
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@whelena whelena left a comment

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Looks good to me but I think there's some lint fixes to be done?

@dan-knight dan-knight requested a review from whelena August 6, 2024 00:11
@dan-knight
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Looks good to me but I think there's some lint fixes to be done?

Fixed!

@dan-knight dan-knight merged commit dc0d7c5 into main Aug 6, 2024
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@dan-knight dan-knight deleted the danknight-nodeless branch August 6, 2024 20:19
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2 participants