Refactored function names in R/plotting.R

[teddyCodex]

Description

Refactored specified function names in R/plotting.R based on issue #7

Original	Modified	User Facing
shorten_lineage	shortenLineage	✅
upset.plot	plotUpSet	✅
lineage.DA.plot	plotLineageDA	✅
lineage.Query.plot	plotLineageQuery	✅
lineage.neighbors.plot	plotLineageNeighbors	✅
lineage.domain_repeats.plot	plotLineageDomainRepeats	✅
LineagePlot	plotLineageHeatmap	✅
LevelReduction	.LevelReduction	✅
GetKingdom	.GetKingdom	✅
stacked_lin_plot	plotStackedLineage	✅
Wordcloud3	plotWordCloud3	✅
wordcloud_element	createWordCloudElement	✅
wordcloud2_element	createWordCloud2Element	✅
lineage_sunburst	plotLineageSunburst	✅
lineage.plot	plotLineage	✅

• perhaps a duplicate: COMMENTED OUT LINEAGE.DA.PLOT this was commented out about 5yrs ago @jananiravi. okay to delete the entire commented out code block?

Fixes issue #51

What kind of change(s) are included?

• [ ] Feature (adds or updates new capabilities)
• [x] Bug fix (fixes an issue).
• [ ] Enhancement (adds functionality).
• [ ] Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

• [x] I have read and followed the CONTRIBUTING.md guidelines.
• [x] I have searched for existing content to ensure this is not a duplicate.
• [x] I have performed a self-review of these additions (including spelling, grammar, and related).
• [x] I have added comments to my code to help provide understanding.
• [x] I have added a test which covers the code changes found within this PR.
• [x] I have deleted all non-relevant text in this pull request template.
• [x] Reviewer assignment: Tag a relevant team member to review and approve the changes.

[teddyCodex]

@the-mayer @jananiravi File containing other locations where the functions are called or referenced.

function_occurrences #51.txt

[the-mayer]

Tagging functions for future review.

The following internal functions should be defined outside of the plotting functions that currently use them. This way, the plot functions can reference these external functions, avoiding the need to define functions within functions.

• .LevelReduction()
• .GetKingdom()