Improvements to PCA, heatmap, and functions that call them

[kelly-sovacool]

Changes

• new function: plot_pca_3d()
• refactor plot_pca() and create calc_pca() for more modular design.
• new option to print diagnostic plots from main workflow functions.
• improve plotting functions for easier use outside of workflow functions.
• create initial draft of visualization vignette.

Issues

• resolves Add NIDAP template - 3DPCA #49
• towards Create visualization vignette #84

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.

[codecov]

Codecov Report

Attention: Patch coverage is 60.79545% with 138 lines in your changes missing coverage. Please review.

Project coverage is 68.67%. Comparing base (aaafe30) to head (35ef62e).

Files with missing lines	Patch %	Lines
R/clean.R	25.92%	40 Missing ⚠️
R/normalize.R	4.76%	40 Missing ⚠️
R/pca.R	67.28%	35 Missing ⚠️
R/histogram.R	61.90%	16 Missing ⚠️
R/filter.R	91.07%	5 Missing ⚠️
R/batch-correction.R	97.43%	1 Missing ⚠️
R/heatmap.R	90.90%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #88      +/-   ##
==========================================
- Coverage   74.03%   68.67%   -5.37%     
==========================================
  Files          15       15              
  Lines         674      798     +124     
==========================================
+ Hits          499      548      +49     
- Misses        175      250      +75     

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