Closed mattssca closed 2 years ago
This PR includes updates to a collection of fancy plots. The following revisions have been made.
fancy_cnbar - Remove lines connecting the dots.
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.
fancy_multisamp_ideogram - Add functionalities to highlight what's different (or shared) between samples. Adding a new parameter that calls cnvKompare if called correctly.
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).
fancy_alignment_plot - Remove lines connecting the dots.
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
Pull Request Checklists
Important: When opening a pull request, keep only the applicable checklist and delete all other sections.
Checklist for all PRs
Required
[x] I tested the new code for my use case (please provide a reproducible example of how you tested the new functionality)
[x] I ensured all dplyr functions that commonly conflict with other packages are fully qualified.
This can be checked and addressed by running
check_functions.pl
and responding to the prompts. Test your code after you do this.devtools::document()
) and addedNAMESPACE
and all other modified files in the root directory and underman
.Optional but preferred with PRs
Checklist for New Functions
Required
[x] I documented my function using ROxygen style.)
[x] All parameters for the function are described in the documentation and the function has a decriptive title.
Example:
import
statment.Example:
Checklist for changes to existing code
[x] I added/removed arguments to a function and updated documentation for all changed/new arguments
[ ] I tested the new code for compatability with existing functionality in the Master branch (please provide a reprex of how you tested the original functionality)