Rmd refactor (part 9) - Githubissues

pdiakumis commented 1 year ago

Ongoing refactoring to harmonise prod with dev as much as possible.

Refac: use sv_prioritize_old and discard empty Genes.
Refac: SV section numbers should match now between master and dev
Feat: replace library_size interactive bar chart with static violin plot
Bug: any requires rowwise in fusions_preprocess
Bug: fusion table hyperlinks fix
Bug: fix oncokb links in summary table (it was still using the master structure with rownames)
Bug: unique takes a vector, else the subsequent args get ignored with no warning (brrr...)

pdiakumis commented 1 year ago

This is finally ready for review @skanwal. I've outlined the changes in the description above, hopefully those make sense. I'll test on several more samples just to be sure in the next couple days. The fusion numbers will differ as discussed.

skanwal commented 1 year ago

@pdiakumis - thanks for tackling this. I am going to test on a case or two as well and post my feedback here.

pdiakumis commented 1 year ago

Thank you @skanwal, I'm aware of those couple things, let's merge for now and I'll do some more tests from my side and we can settle on next steps next week ;-)

umccr / RNAsum

Rmd refactor (part 9) #121