metabo-usecases

Reproducible pipeline that regenerates every figure and table for the OmniPath Metabo manuscript — main text and supplementary — from a pinned OmniPath Postgres snapshot.

The repository is structured as an R package (metabo.figures) with adjacent figure/table workspace directories, Python helpers under python/, LaTeX composite-assembly + caption sources under tex/, manual vendored assets under inst/extdata/manual/ (including the Figure 1 Panel A architecture PDF/SVG authored in Inkscape), and a single top-level rebuild entrypoint.

Quick start

ssh -p 2323 omnipath@omnipathdb.org   # development happens on beauty
cd ~/dev/metabo-usecases
./rebuild.sh --dry-run                 # print the work plan
./rebuild.sh --png --bundle --check    # full rebuild with checks
tail -f logs/latest.log                # follow the unified pipeline log

See the full quickstart and contracts in the saezverse spec:

• Spec: saezverse/ai/specifications/omnipath-metabo-figures/specs/001-figures-pipeline/spec.md
• Plan: …/plan.md
• Quickstart: …/quickstart.md
• Contracts: …/contracts/

Deliverables

• Figure 1 — workflow-architecture diagram (manual Inkscape asset, vendored under inst/extdata/manual/architecture/) + quantitative database-content panels
• Figure 2 — webapp screenshots (manual asset)
• Figure 3 — MetalinksDB v1 vs v2 comparison
• Figure 4 — old vs new COSMOS PKN comparison + included schematic graphics
• Figure 5 — lung-cancer use case (refactored from omnipath_metabo_case1)
• Tables — ID resolving (Methods), RaMP comparison (Methods), supplementary tables
• Optional manuscript bundle: a single PDF concatenating every artifact in submission order

Conventions

• R code style: follows human/guidelines/r-coding-style.md in the saezverse repository (roxygen2 docstring order, < 80-char lines, hanging closing parens, pipes over intermediate variables, snake_case with no get_ prefix, logger::log_* for output, @importFrom per function, single implicit return).
• Trunk-based development on main; the UseCase2 branch is a backup for future case studies and is not pulled into main.
• Logging: every R, Python, bash, and captured xelatex line writes to one file pointed at by METABO_FIGURES_LOG; line format in contracts/log-format.md.
• Reproducibility: every artifact emits a provenance sidecar; per-build manifests and snapshot identifiers are written to manifests/.

License

BSD 3-Clause — see LICENSE.