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feat: added pixi env and R circos plot example#7

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finstermeier merged 7 commits intomainfrom
dev
Apr 13, 2026
Merged

feat: added pixi env and R circos plot example#7
finstermeier merged 7 commits intomainfrom
dev

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@m-jahn m-jahn commented Apr 8, 2026

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Copilot AI review requested due to automatic review settings April 8, 2026 14:45
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Pull request overview

Adds an R-based Circos plotting example to the repo and introduces a pixi environment to make running the notebook reproducible.

Changes:

  • Added source/circlize.R with helper functions to validate genomic coordinates, compute GC metrics, and generate a circlize genome plot.
  • Added pipeline/plot_circos.Rmd tutorial notebook and linked it from the README.
  • Added pixi.toml/pixi.lock plus git config updates to support a circlize pixi environment.

Reviewed changes

Copilot reviewed 5 out of 8 changed files in this pull request and generated 8 comments.

Show a summary per file
File Description
source/circlize.R New plotting utilities (validation, GC metrics, circlize tracks).
pipeline/plot_circos.Rmd New R notebook demonstrating how to generate the plot using the utilities.
README.md Adds link to the new rendered circlize notebook.
pixi.toml Defines a circlize feature/environment and a render task for the notebook.
pixi.lock Locks the pixi environment for reproducible installs.
.gitignore Ignores local .pixi/ environment files (except config).
.gitattributes Marks pixi.lock as generated/binary merge behavior and adjusts linguist settings.

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Comment thread source/circlize.R Outdated
Comment thread source/circlize.R Outdated
Comment thread source/circlize.R Outdated
Comment thread source/circlize.R
Comment thread pipeline/plot_circos.Rmd Outdated
Comment thread pipeline/plot_circos.Rmd Outdated
Comment thread pipeline/plot_circos.Rmd Outdated
Comment thread pixi.toml Outdated
@m-jahn m-jahn requested review from finstermeier and rabioinf April 10, 2026 17:53
@finstermeier finstermeier merged commit 3aafa95 into main Apr 13, 2026
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3 participants