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Add wide option to tbl_genomic() #341

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karissawhiting wants to merge 26 commits into
MSKCC-Epi-Bio:mainfrom
slb2240:tbl_genomic_wide
Open

Add wide option to tbl_genomic() #341
karissawhiting wants to merge 26 commits into
MSKCC-Epi-Bio:mainfrom
slb2240:tbl_genomic_wide

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@karissawhiting karissawhiting commented Mar 7, 2024

What changes are proposed in this pull request?

To-do's before merging

  • Bring in any comments over from other PR and close that PR (Tbl genomic wide #307). All code changes should already haved moved - @hfuchs5
  • Add proper class tbl_wide (for add_q) - @karissawhiting
  • Split out wide code in a separate internal function - @slb2240
  • Check speed (consider checking base R options. See Sammi's notes. We should only change if it's slow. If speed is reasonable, let's stick with tidyverse options as they are easier to read) - @hfuchs5
  • Update docs of both tbl_genomic and add_q -@slb2240
  • Test with a by variable - @karissawhiting
  • Make sure unit tests run (after above are addressed) - later

If there is an GitHub issue associated with this pull request, please provide link.


Reviewer Checklist (if item does not apply, mark is as complete)

  • PR branch has pulled the most recent updates from main branch. Ensure the pull request branch and your local version match and both have the latest updates from the main branch.
  • If a new function was added, function included in _pkgdown.yml
  • If a bug was fixed, a unit test was added for the bug check
  • Run pkgdown::build_site(). Check the R console for errors, and review the rendered website.
  • Code coverage is suitable for any new functions/features. Review coverage with withr::with_envvar(new = c("NOT_CRAN" = "true"), covr::report()). Begin in a fresh R session without any packages loaded.
  • R CMD Check runs without errors, warnings, and notes
  • usethis::use_spell_check() runs with no spelling errors in documentation

When the branch is ready to be merged into master:

  • Update NEWS.md with the changes from this pull request under the heading "# cbioportalR (development version)". If there is an issue associated with the pull request, reference it in parentheses at the end update (see NEWS.md for examples).
  • Run codemetar::write_codemeta()
  • Run usethis::use_spell_check() again
  • Approve Pull Request
  • Merge the PR

slb2240 and others added 26 commits April 26, 2023 09:57
This reverts commit 8b4e436.
Getting the following error:
Error in get_theme_element("pkgwide-lgl:quiet") :
could not find function "get_theme_element"
`tbl_genomic()` wide was using too much time on the `summarize_by_gene()` so I made `.remove_endings()`. it's still slow but here is the tictoc now:

`tic()
             tbl1 <- tbl_genomic(gene_binary, wide = T)
 toc()`
76.4 sec elapsed
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3 participants