place main viewplot in the center

[whelena]

Description

Original: main clone vp is set so that the top is aligned with y = 0.9. This works great with default plotting.direction = 'down', but not the other direction. Setting back to defaults, which works better

Small example

Top = before, bottom = after

Larger example

Left = before, right = after

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]

this is an improvement but obviously not ideal, I thought of two approaches that might work:

1. Change the alignment on the viewport based on the plotting.direction, defaulting to centered when an angle/number is used to avoid complication.
2. In the save.plot function, draw the grob inside a viewport that can be moved around using user defined params. Want to avoid this since it puts to much responsibility on the user (not user-friendly)

I think these two approaches are similar, would benefit from someone who understands viewports better - @dan-knight

[dan-knight]

I think we could refine this a tiny bit. All plotting directions are just an angle under the hood. For example, right is just a convenient way to set the plotting angle to 90. I think the start could simply rotate around the center based on the underlying plotting.direction number. Then, down/0 would be unchanged, but other plotting directions would be adjusted accordingly.

[whelena]

Ya we could try that, what about weirder angles like 45 or 60? SHould we just collapse them to the nearest direction?

[dan-knight]

Ya we could try that, what about weirder angles like 45 or 60? SHould we just collapse them to the nearest direction?

Still works! Imagine a circle around the plot center point. The starting node would just rotate continuously along that circle with whatever plotting direction angle is specfied (45, 60, 31, 0.00151, anything).

[whelena]

Shifted the plot downward in calculate.main.plot.size to ensure all content is visible. Ideally, we'd set yscale = c(ymax, ymin) in the make.plot.viewport function (currently unsupported). Additionally, doing that distorts other plot component (normal node placement). I think it's due to how viewports are layered throughout.

I propose we mark this as a potential future fix for cleaner scaling and merge this after fixing the tests?