Part3 Freec as default: Oncoprint update

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

We updated the consensus seg file creation in AlexsLemonade#987 to use freec CN calls as default .
A re-run focal-cn-file-preparation updated results/consensus_seg_most_focal_cn_status.tsv.gz in AlexsLemonade#988 .
In this PR we will use the updated consensus_seg_most_focal_cn_status.tsv.gz as input and re-create the oncoplots.

What was your approach?

Just run run-oncoprint.sh

What GitHub issue does your pull request address?

related to AlexsLemonade#964

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

There are no drastic changes it seems to me.

However , since in #2 we start seeing that majority of the changes are losses that are now gains , I also see all the losses change to gains in the oncoplot!!

Figure in this branch
https://github.com/kgaonkar6/OpenPBTA-analysis/blob/oncoprint/analyses/oncoprint-landscape/plots/all_participants_primary_only_goi_oncoprint.png

Figure in master branch
https://github.com/kgaonkar6/OpenPBTA-analysis/blob/master/analyses/oncoprint-landscape/plots/all_participants_primary_only_goi_oncoprint.png

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.