seekit

Shared R helpers for the Wing Lab — plotting, save helpers, SCE handling.

This package consolidates the helper .R files that used to be vendored as per-project R/<name>.R copies across ~/My Drive/Wing Lab/. One canonical source, version-locked per project via renv for reproducibility.

Install

In a project's R session:

# one-time, per machine:
install.packages("remotes")

# pin to a specific commit/tag (reproducible):
remotes::install_github("david-priest/seekit@v0.0.0.9000")

# or floating to main (will pick up updates on next install):
remotes::install_github("david-priest/seekit")

For reproducibility, use renv in each analysis project:

# in the project root:
renv::init()
renv::install("david-priest/seekit")
renv::snapshot()       # records the commit hash in renv.lock — commit it

When a helper gets fixed and you want this project to pick up the fix:

renv::update("seekit")
renv::snapshot()       # commits the updated lock — old projects untouched

Use

library(seekit)
# every helper is exported under its function name:
f2(...)
plotDR1(...)
saveFig(...)

Development workflow

1. Edit a helper here in R/.
2. Test locally: devtools::load_all() to source everything; f2(...) etc.
3. Commit + push. GitHub Actions runs R CMD check on every push and once a day to catch upstream CRAN breakage.
4. To cut a release: bump Version: in DESCRIPTION, tag the commit (git tag v0.0.1; git push --tags). Projects can pin to the tag.

Importing helpers from the Wing Lab tree

The initial population of R/ was done by tools/import_from_my_drive.R — a re-runnable script that scans ~/My Drive/Wing Lab/ for **/R/*.R, picks the newest-mtime copy of each helper, and copies it in. Re-run to bring in newer in-the-wild versions during the transition period (until every project has switched to importing the package and stopped editing vendored copies):

Rscript tools/import_from_my_drive.R

The script lists the helpers it includes vs. skips (one-off project-specific files like gsea_*.R are skipped — they don't belong in a shared package).

Status

Pre-roxygen. Functions are exported via a catch-all exportPattern in NAMESPACE. Adding @param / @export / @return roxygen comments per function is a follow-up — once done, devtools::document() generates a clean NAMESPACE and man/ pages.

R CMD check will throw "no visible binding for global variable" warnings on unqualified dplyr::/ggplot2:: calls inside helpers. These are cosmetic during the transition; cleanup is gradual.

Related

• wing-lab-R-helpers — the older wlrh CLI that syncs vendored copies across projects. Use it for migrating helpers OUT of projects (replace R/<name>.R with library(seekit)) but wlrh push is now disabled by default to prevent surprise overwrites.