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Standardize batch correction figure behavior across function calls#4

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phoman14 wants to merge 10 commits into
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FigOutSync
Open

Standardize batch correction figure behavior across function calls#4
phoman14 wants to merge 10 commits into
mainfrom
FigOutSync

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@phoman14

@phoman14 phoman14 commented Jul 6, 2026

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Changes

  • Install CCBR/MOSuite from the FigOutSync branch during setup and sync the vendored code/MOSuite package to the same updated batch_correct_counts() figure behavior before the next released image/package update.
  • Load the vendored /code/MOSuite package at runtime with devtools::load_all('/code/MOSuite'), matching capsules where the package code is available in code/MOSuite.
  • Expose the updated batch correction PCA, histogram, correlation heatmap, interactive plot, sample rename, and color controls in both the CLI and Code Ocean app panel.
  • Use the hardcoded MOSuite color palette as the capsule default so package and capsule figure defaults stay aligned.
  • Keep the CLI compatible with older installed MOSuite versions by forwarding new plotting arguments only when batch_correct_counts() supports them.
  • Add tests for the FigOutSync package install, updated CLI arguments, and app panel parameters.
  • Add @phoman14 attribution to the development changelog entries for this PR.

Issues

No linked issue.

PR Checklist

  • This comment contains a description of changes with justifications, with any relevant issues linked.
  • Run the capsule in Code Ocean and ensure it completes successfully with no errors.
  • Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Follow the style described in https://style.tidyverse.org/news.html
  • The tests workflow succeeds on the latest commit.

Validation:

  • Rscript tests/testthat.R (PASS 30)
  • Rscript -e 'jsonlite::fromJSON(".codeocean/app-panel.json")'
  • git diff --check

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