Node spread

[dan-knight]

Description

Adds the spread column to the input tree dataframe, allowing node-by-node spread. This calculation is proportional to the automatically calculated angles, so a value of 1.5 will increase the distance between neighbouring nodes by 50%. Likewise, a value below 1 such as 0.85 will reduce the distances by 15%.

These changes also include updates to documentation and regression test cases.

Examples

Inner Node Spread

tree.input <- data.frame(
    parent = c(NA, 1, 1, 1, 1),
    spread = 1
    );
# Second child node from the left
tree.input$spread[3] <- 2;

grid.draw(
    SRCGrob(tree.input)
    );

Outer Node Spread

tree.input <- data.frame(
    parent = c(NA, 1, 1, 1, 1),
    spread = 1
    );
# Rightmost node
tree.input$spread[5] <- 2;

grid.draw(
    SRCGrob(tree.input)
    );

Mixed Spread

tree.input <- data.frame(
    parent = c(NA, 1, 1, 1, 1),
    spread = 1
    );
tree.input$spread[3:5] <- c(1, 0.5, 2);

grid.draw(
    SRCGrob(tree.input)
    );

Checklist

• [X] 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 problem[^1] - Even a small leak can be costly[^2].

• [X] This PR does NOT contain germline genetic data[^3], RNA-Seq, DNA methylation, microbiome or other molecular data[^4].

[^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.

• [X] 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.

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

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

• [X] 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].

• [X] 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.