Standardize output figures across MOSuite function calls

[phoman14]

Summary

This PR standardizes the appearance of MOSuite output figures across direct plotting calls, workflow calls, and the matching Code Ocean capsules. The intent is that the same data and grouping metadata produce consistent colors, category order, point sizing, and readable legends whether a figure is created by plot_pca_2d(), plot_pca_3d(), plot_histogram(), filter_counts(), normalize_counts(), or an affected capsule.

Changes

• Set the user-facing MOSuite plot color defaults to match the current capsule defaults, while keeping get_mosuite_colors() available for later use.
• Preserve random color generation only as a fallback when a selected or provided palette has too few colors for the observed groups or samples.
• Resolve group color order from factor levels for factor columns, and from first appearance in metadata for non-factor columns.
• Share PCA and histogram legend layout behavior so top and bottom legends wrap and scale text for many or long labels instead of clipping.
• Align PCA and histogram defaults used by filter_counts() and normalize_counts() with the defaults exposed by the affected capsules.
• Add focused tests for color resolution, PCA legends, histogram legends, filter defaults, and normalize defaults.
• Update documentation and NEWS.md for the user-facing figure default changes.

Affected capsule repos from these package changes:

• NIDAP-Community/MOSuite-filter-counts: Standardize filter output figures across MOSuite function calls NIDAP-Community/MOSuite-filter-counts#3
• NIDAP-Community/MOSuite-normalize-counts: Standardize normalize output figures across MOSuite function calls NIDAP-Community/MOSuite-normalize-counts#4
• NIDAP-Community/MOSuite-plot-pca-2D: Standardize 2D PCA output figures across MOSuite function calls NIDAP-Community/MOSuite-plot-pca-2D#2
• NIDAP-Community/MOSuite-plot-pca-3D: Standardize 3D PCA output figures across MOSuite function calls NIDAP-Community/MOSuite-plot-pca-3D#2

Validation:

• test-plot_pca.R: PASS 21
• test-plot_histogram.R: PASS 14
• test-filter.R: PASS 27
• test-normalize.R: PASS 22
• Rd syntax validations passed for updated PCA/histogram docs.

Issues

No linked issue.

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• Write unit tests for any new features, bug fixes, or other code changes.
• Update the docs if there are any API changes (roxygen2 comments, vignettes, readme, etc.).
• Update NEWS.md with a short description of any user-facing changes and reference the PR number. Follow the style described in https://style.tidyverse.org/news.html
• Run devtools::check() locally and fix all notes, warnings, and errors. Focused package tests passed; full devtools::check() was not run in this session.

[codecov]

Codecov Report

❌ Patch coverage is 86.73469% with 26 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.71%. Comparing base (ce1865a) to head (42c8cb3).
⚠️ Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
R/plot_heatmap.R	57.14%	9 Missing ⚠️
R/filter.R	62.50%	6 Missing ⚠️
R/plot_pca.R	80.64%	6 Missing ⚠️
R/plots.R	90.90%	4 Missing ⚠️
R/colors.R	97.77%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #223      +/-   ##
==========================================
+ Coverage   79.66%   79.71%   +0.04%     
==========================================
  Files          22       22              
  Lines        3398     3534     +136     
==========================================
+ Hits         2707     2817     +110     
- Misses        691      717      +26     

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