Enhance plotting functions and documentation

[AbhirupaGhosh]

Updated documentation for plotPRC, plotROC, plotCM, plotDensity, and plotTopFeatsVI functions. Added new functions for plotting ROC curves, confusion matrices, and density of predicted class probabilities.

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• 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).

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[epbrenner]

These work, but I'd strongly suggest that the import functions for the plots to natively include the tsv reading rather than requiring it.

[AbhirupaGhosh]

These work, but I'd strongly suggest that the import functions for the plots to natively include the tsv reading rather than requiring it.

I have modified the function to input tsv.
I have added additional plotting functions based on my Staph poster and a few others. @eboyer221, please look through the plots to decide if anything can be adapted for the dashboard or generate an Rmd as the end product of amRml.

[eboyer221]

@AbhirupaGhosh @jananiravi @amcim
I am currently reviewing these plots and working on adding them into the amRviz dashboard, along with an option to export them. Since plotCrossDrug() uses ComplexHeatmap, bringing that into amRviz will give us a Bioconductor dependency we need, which should help resolve the BiocCheck warning we have been hitting in that package.