Part4 Freec as default: Chromosome wide CNV plots per histology

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

Similar to #3 we are propogating the changes proposed in AlexsLemonade#987 to use freec CN calls as default to some modules that plot the CNV changes.
In this PR we will use the updated consensus_seg_most_focal_cn_status.tsv.gz from #2 as input to recreate chromosome wide plots.

What was your approach?

Just re-run cn_status_heatmap.Rmd and gistic_plot.Rmd

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?

Not sure which data release was used to generate these plots before but there are some histologies (like "CNS neuroblastoma" ) which have now been renamed (Neuroblastoma) so please be keep a note of that while tracking files that have/have ot changed by this update.

There are also sample number changes which are not related to the update here but are dependent on data release.

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

Results

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

Yes

What is your summary of the results?

I continue to see gains (because I guess I'm looking for those) in the updated files for example chr15 in LGAT_plot.png didn't have any gain in the plot in master branch but the file in this branch does have gains.

file in chrom_plot branch

file in master branch

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.