Polygon parameters

[whelena]

Description

Exposes parameters for more detailed control of fishplot polygon styles, including color, alpha, and polygon shape. Parameter names were changed to prefix polygon.<parameter> for clarity and consistency. polygon.width was changed to polygon.scale, which now functions as a multiplier rather than an objective value.

Expands the colour scheme control to create a gradient from an arbitrary list of colors (not just one). This serves as the default polygon. This color scheme can be overridden for individual nodes using the polygon.col column in the tree input dataframe. This clarifies the usage of each parameter and removes the existing overlap in their use-cases.

Results

SRCGrob(
    data.frame(
        parent = c(NA, 1, 2, 3, 2),
        CP = c(1, 0.8, 0.3, 0.03, 0.21)
        ),
    polygon.colour.scheme = c('lightblue', 'pink', 'orange'),
    add.normal = TRUE,
    polygon.scale = 1.5
    );

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]

Yeeeouch! High contrast colors in the example! Alpha is definitely 1 haha!

LGTM. I'll just add some extra validation and tests to follow the other parameters.

[whelena]

Lgtm! Since I opened the PR I think you have to give your approval to merge.

[whelena]

@dan-knight One of the test case failed after merging the main branch. Can you double check to make sure it still works properly after the merge?

[dan-knight]

@whelena I added more changes here. Take a look and let me know if there's anything else you'd change. Otherwise, I can approve and merge.

[whelena]

Typo?

[whelena]

Is this still supported? Does this mean assigning node-specific polygon colours can be done through this or the dataframe?
Maybe we should add the different ways users can assign polygon colours and how we recommend using them.

[dan-knight]

True, I'll add to this section first and see if I can clear it up for you in the User Guide. Will be a good test of the docs.

[whelena]

@whelena I added more changes here. Take a look and let me know if there's anything else you'd change. Otherwise, I can approve and merge.

Everything looks good, I just have a few clarification questions about the different was we can specify polygon colours.

[dan-knight]

Approving on behalf of both myself and @whelena, since we both contributed code and reviewed.