Remove R script/notebook package installs from snv-callers (Part 2 of N)

[cansavvy]

Purpose/implementation Section

What was your approach?

I'm removing R package installations in the scripts in accordance with #690
I'm keeping track of the PRs I file for that issue there.

This PR is me having going through snv-callers by its own because its a large one and has notebooks that require a lot of memory usage.

• Removed package installs from compare_snv_callers_plots.Rmd and compare_snv_callers_plots-tcga.Rmd
• Removed the VAF correlation plot from snv-callers, its very memory intensive and was crashing things out. Changed it to a table.
• Changed the output file for pbta data plots to pbta-comparison so its more parallel to tcga-comparison.
• Set up AWS instance.
• Reran both notebooks.
• Committed and pushed results files

Note that I'm ignoring the vaf_cutoff_experiment.Rmd notebook since it is deprecated.

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

Everything look okay? (Note this does not address #700 I'm looking into that separately).

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

Yes, but the results shouldn't really be different.

Reproducibility Checklist

No changes are needed here.

• 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.

[cbethell]

LGTM @cansavvy! 👍

[jaclyn-taroni]

It looks to me like there are some differences in the plots - any ideas why that might be? Are these portions of the snv-callers pipeline that didn't get rerun after some data release?

[cansavvy]

It looks to me like there are some differences in the plots - any ideas why that might be? Are these portions of the snv-callers pipeline that didn't get rerun after some data release?

Yes. The compare notebook (because it takes so much memory) doesn't automatically get run in the pipeline scripts, there's an option to turn it on or off:

OpenPBTA-analysis/analyses/snv-callers/run_caller_consensus_analysis-pbta.sh

Line 79 in 0985505

if [ "$run_plots_nb" -gt "0" ]

So I think it been a tad since these notebooks got run fully.