Circular angle calculations

[dan-knight]

Description

Fixes a bug in the refactored angle calculation code to return to the original "circular" behaviour of the v1 algorithm. Before this, child angles were calculated beginning at 0 degrees, meaning that levels moved directly "downward". This creates two problems for users:

1. Trees will naturally be more congested as nodes "bunch up" in the middle.
2. More angles will need to be overridden by the user to address this issue.

These changes mean that the user needs to specify far fewer angles to handle crowded trees. For many use cases, the automatic angle calculation will create a well-spaced tree. Beyond this, often only one or two angles in the first level of the tree need to be overridden to create ample visual space for lower levels with many nodes.

These changes have removed the existing override.angles() function, but I haven't yet deleted the code as it be useful in the future (perhaps for handling edge cases).

Examples

radial

tree.df <- data.frame(
    parent = c(NA, 1, 2, 2, 3, 3, 3, 3, 8, 8, 8, 10, 10, 11),
    angle = NA
    );
tree.df$angle[3] <- -90;
tree.df$angle[8] <- -40;

tree <- SRCGrob(tree.df);
grid.draw(tree);

fixed

tree.df <- data.frame(
    parent = c(NA, 1, 2, 2, 3, 3, 4, 4, 6, 7, 10, 10, 7),
    angle = NA
    );
tree.df$angle[3:4] <- c(-60, 60);

tree <- SRCGrob(tree.df);
grid.draw(tree);

Closes #122

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]

I see that there are two fucntion to calculate angles (calculate.angles.radial and calculate.angles.fixed) Althought in the exmaples you showed the two SRCGrob calls look the same. How do users choose which function to use?

[dan-knight]

I see that there are two fucntion to calculate angles (calculate.angles.radial and calculate.angles.fixed) Althought in the exmaples you showed the two SRCGrob calls look the same. How do users choose which function to use?

They don't! Those are all handled internally depending on the complexity of the tree. The two methods are becoming very similar anyway, so I think it would be good to combine them before releasing v3. For now, I'm just accounting for both.