Chromothripsis v21 update

[LauraEgolf]

Purpose/implementation Section

What scientific question is your analysis addressing?

Update chromothripsis module from v19 to v21 data (v20 update included changes to CNV consensus data, which affects ShatterSeek analysis).

What was your approach?

• Adjusted 02-run-shatterseek-and-classify-confidence.R to work with new format for CNV consensus data (filled in NA values with tumor ploidy). Also added a couple debugging updates.
• Updated 03-plot-chromothripsis-by-histology.Rmd with new plots for cancer_group. Also updated all plot titles for clarity.
• Adjusted 04-plot-chromothripsis-and-breakpoint-data.html to accommodate increased number of chromothripsis calls (code should be more flexible now).

What GitHub issue does your pull request address?

1122 (see also: #1007)

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

Which areas should receive a particularly close look?

N/A

Is there anything that you want to discuss further?

N/A

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

Yes - the figure going into the manuscript will probably be plots/03-histology/chromothripsis_proportion_by_cancerGroup.pdf but we should discuss further. I still plan to finish out the module by adding a couple scripts to visualize candidate chromothripsis regions, but I don't think this will affect any of the results I've submitted so far.

Results

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

Updated all tables and figures. Added 2 new figures under 03-histology showing breakdown by cancer_group.

What is your summary of the results?

The updated CNV consensus data resulted in more chromothripsis calls (specifically, the # CNVs increased when the stringency for reciprocal CNV overlap was reduced, so ShatterSeek detected more CN oscillations). Previous results showed 64/777 tumors with chromothripsis; we are now seeing 87/777 tumors. Otherwise, most of the results look very similar. (See notes from previous PRs: #1098, #1106).

Reproducibility Checklist

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

Documentation Checklist

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

[jharenza]

Hi @LauraEgolf ! thanks for adding this. Could you convert the figures to png instead of pdf? Thanks!

[jharenza]

@LauraEgolf can you also add a linear regression line + R and p-value to this plot: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/084c0e13ee17561587e360406dac0fa195050f40/analyses/chromothripsis/plots/04-breakpoint-data/count_chromothripsis_cnv_and_sv_breaks_scatterplot.pdf - this is great!

and legends to the # of SV or CNV breaks vs chromothripsis regions plots - those are really nice!

[LauraEgolf]

@jharenza Sounds great, I will make those changes today or tomorrow.

and legends to the # of SV or CNV breaks vs chromothripsis regions plots - those are really nice!

For this, do you mean a legend for the fill? The fill just corresponds to the # chromothripsis regions, which is shown on the x axis. I can still add a legend if you want though.

[jharenza]

For this, do you mean a legend for the fill? The fill just corresponds to the # chromothripsis regions, which is shown on the x axis. I can still add a legend if you want though.

Oh yes but in that case, then you don't need a color for the fills. Thanks!