Fancy Plots + QoL Updates

[mattssca]

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[mattssca]

This PR includes updates to a collection of fancy plots. The following revisions have been made.

1. fancy_cnbar - Remove lines connecting the dots.

2. fancy_ideogram - New parameter that allows the user to subset calls to regions specified in a bed-like format. For more info and how to use it, see the newly added parameters and descriptions.

3. fancy_multisamp_ideogram - Add functionalities to highlight what's different (or shared) between samples. Adding a new parameter that calls cnvKompare if called correctly.

4. fancy_circosplot - Circos plot now takes additional variant call sets. Previously it only plotted manta calls, but can now be run so that ssm calls are plotted (similarly to other fancy plotting functions).

5. fancy_alignment_plot - Remove lines connecting the dots.

6. fancy_qc_plot - Barplot has now been replaced with boxplot + jitter for visualizing QC metrics across different sample cohorts, pathologies, etc.

This PR also includes a few minor QoL updates. Including an update to cnvKompare to always retain the same columns in the returns (regardless if concordant or discordant calls are returned) as well as a hot-fix to collate_results (see issue 112).

Before review of this PR, I want to include one more commit I am working on as well as some more thorough testing of the updated plotting functions. I will call for reviewers when the PR is ready to be reviewed

[Kdreval]

Can you please give an idea on what the GenomicRanges are used for? If it is just to overlap the coordinates, we can consider using the foverlaps and avoid adding another big-sized dependecy

[mattssca]

Indeed, the GenomicRanges package is used for intersecting two bed-like files. I will revert this to using foverlaps as suggested above. Thanks!

[Kdreval]

Alright, see it here now! Can we consider switching this to data.table::foverlaps()?

[mattssca]

Yes, I will do this. Good suggestion!

[Kdreval]

nice addition 😄