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)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

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[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()

[the-mayer]

I made some small adjustments, based on other incoming PRs.

Thanks for your contribution @teddyCodex