Oncoprint update

[runjin326]

Purpose/implementation Section

What scientific question is your analysis addressing?

Modified oncoprint to: 1) Modified NA to Not done 2) Added mutation_status annotation as indicated in https://github.com/d3b-center/Cole-telomere-analysis/issues/16

What was your approach?

1) for modifying NA:

hgat <- hgat %>%
  dplyr::left_join(tmb) %>%
  dplyr::mutate(`C-circle` = case_when(
    `C-circle` %in% c("POS", "NEG") ~ `C-circle`,
    TRUE ~ "Not done"
  )) 

2) For adding TMB, I used TMB from OpenPBTA-analysis/analyses/tmb-compare/TMB_d3b_code/outputs/pbta-snv-consensus-TMB_intarget.txt and used

  dplyr::mutate(
    mutation_status = case_when(
      TMB < 10 ~ "Normal",
      TMB >= 10 & TMB < 100 ~ "Hypermutant",
      TMB>= 100 ~ "Ultra-hypermutant")
  )

What GitHub issue does your pull request address?

https://github.com/d3b-center/Cole-telomere-analysis/issues/16

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

Which areas should receive a particularly close look?

Please double check the following: 1) Do we like the color for "Not done"? 2) Is it right to use the OpenPBTA output? 3) Looks like mutation_status only has "Normal" (TMB <10).

Also note that this is a staggered PR, so would clean up once the re-run PR is merged.

Is there anything that you want to discuss further?

No.

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)?

New oncoprint plot

What is your summary of the results?

NA.

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.

[jharenza]

Tmb to use should be Tmb in the data release called pbta coding Tmb, not the module data- that module is deprecated.

[runjin326]

@jharenza - thanks. Updated now.

[runjin326]

@jharenza - all recommended changes implemented.