Horizontal dendrogram and polygon plot

[whelena]

Description

Horizontal dendrogram support: Extended create.phylogenetic.tree to support plotting.direction = 'left' and 'right', rotating polygons, nodes, and edges so fish plots can be rendered in any of the four cardinal directions.
Axis placement fixes: Rewrote calculate.main.plot.size to derive viewport bounds directly from actual node/clone coordinates across all directions (removing direction-specific padding logic), and updated make.plot.viewport to store and use ylims so the yscale is correct for rotated plots.
Axis label positioning: Fixed add.axis.label in set.up.plot.area.R so that axis labels for all four positions (top, bottom, left, right) are placed at a consistent physical gap from the outer edge of the tick marks, accounting for tick length explicitly via convertX/convertY on the tick grob.
Text placement for horizontal plots: Updated add.text2 / position.node.text in add.text.R to apply xline.dist in the y direction for 'left'/'right' plots (perpendicular to horizontal branches) while keeping text glyphs always horizontal (rot = 0). Fixed degenerate slope computation for horizontal branches.

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]

Repo name warning will be addressed separately