Contributing to Cellucid (R package)#

The cellucid-r package exports data to the same on-disk format used by the Cellucid viewer.

If you are editing the R package itself, the canonical contribution guide lives in the cellucid-r repo (cellucid-r/CONTRIBUTING.md). This page mirrors that guidance so contributors can find it from the main documentation site.

Which repo should I contribute to?#

Cellucid is split by responsibility:

Repo

What it is

Contribute here when you…

cellucid

Web app (UI + state + WebGL rendering)

are fixing UI bugs, rendering/performance, figure export, sessions, or community annotation frontend

cellucid-python

Python package + CLI (prepare, serve, show_anndata, hooks) + Sphinx docs

are fixing Python/CLI bugs, data prep/export, server endpoints, Jupyter hooks, or docs on ReadTheDocs

cellucid-r

R package for exporting data to the Cellucid viewer format

are changing the R exporter (cellucid_prepare()), adding R-side tests/docs, or preparing for Bioconductor

cellucid-annotation

GitHub repo template for community annotation

are changing the repo schema/validation/workflows

If you’re not sure where a bug belongs, open an issue in the repo you’re currently using and include:

  • how you loaded data (exports vs h5ad/zarr vs remote server vs Jupyter),

  • the UI environment (hosted app vs local app vs Jupyter iframe),

  • and the smallest reproduction you can share.

Fast paths (pick your contribution type)#

I want to report a bug#

Please include:

  • R version (R.version.string)

  • OS (macOS/Windows/Linux)

  • how you generated exports (which function call, which inputs)

  • expected vs actual behavior

  • the smallest dataset you can share (prefer synthetic/reproducible)

  • any R CMD check output if relevant

If the bug is “the viewer looks wrong”, also include:

  • which viewer environment you used (hosted app vs local app vs Jupyter iframe)

  • browser + version

  • whether you loaded the export via browser file picker vs remote server vs GitHub exports

I want to contribute docs only#

Docs live in:

  • cellucid-r/man/ (generated .Rd files)

  • cellucid-r/vignettes/ (BiocStyle vignette)

  • cellucid-r/README.md

If you edit .Rd files directly, be aware they are usually generated from roxygen comments in cellucid-r/R/. Prefer editing roxygen in R/ and re-running devtools::document().

I want to add/modify R code#

Fast workflow:

  1. Set up your R dev environment (see “Development setup”)

  2. Make a small, focused change

  3. Add/adjust tests (testthat)

  4. Run devtools::check() (and BiocCheck::BiocCheck() if relevant)

  5. Submit a PR with a clear “what/why/how to verify”

Development setup (cellucid-r)#

Prerequisites#

  • R >= 4.3.0 (matches DESCRIPTION)

  • Git

Recommended:

  • RStudio (optional, but convenient for vignettes)

  • Pandoc (needed for some vignette builds; RStudio bundles it)

Install dev tools#

In R:

install.packages(c("devtools", "roxygen2", "testthat"))

For vignette builds and Bioconductor-style docs:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install(c("BiocStyle", "knitr", "rmarkdown"))

Optional (useful during release prep):

BiocManager::install("BiocCheck")
install.packages(c("pkgdown", "covr"))

Install package dependencies:

devtools::install_deps(dependencies = TRUE)

Load the package from source (fast inner loop):

devtools::load_all()

Tests#

Run tests:

devtools::test()

Run a full check (recommended before PRs):

devtools::check()

For Bioconductor submission readiness:

BiocCheck::BiocCheck(".")

Guidelines:

  • Add tests when behavior changes (especially edge cases like missing values, mismatched dimensions, sparse matrices).

  • Prefer small synthetic inputs; avoid committing real datasets.

Documentation (roxygen + vignettes)#

Regenerate .Rd files#

Most man pages should be generated from roxygen comments in cellucid-r/R/.

devtools::document()

Build vignettes#

devtools::build_vignettes()

pkgdown site (optional)#

If you’re working on the website output (GitHub Pages):

pkgdown::build_site()

Design constraints (important for contributors)#

This package is intentionally:

  • minimal-dependency (only jsonlite is a hard dependency)

  • format-first (exports must match what the web app expects)

  • Bioconductor-friendly (checks, vignette style, and package structure matter)

If you propose adding a new dependency:

  • prefer Suggests over Imports unless strictly required

  • keep the core exporter usable on minimal installations

If you change the export format or schema:

  • coordinate with cellucid-python and the web app (cellucid) so the ecosystem stays compatible

  • add tests that validate the new behavior

How to validate exports end-to-end#

The most reliable validation is to export a tiny dataset and load it in the viewer.

Recommended workflow:

  1. Run cellucid_prepare() on a tiny synthetic dataset.

  2. Open the Cellucid web app (hosted or local).

  3. Use “Browse local data…” and select the export folder.

  4. Confirm:

    • the correct number of cells render

    • categorical and continuous fields appear

    • gene expression search works (if exported)

This catches many “format is technically written but semantically wrong” issues.

PR guidelines#

  • Keep PRs small and focused (one feature/bugfix at a time).

  • Include:

    • what changed

    • why it changed

    • how to verify (commands + expected outcome)

  • If user-facing behavior changes:

    • update docs (README/vignette/man page as appropriate)

    • add/adjust tests

    • consider updating NEWS.md if it’s release-notable

Troubleshooting (common contributor problems)#

devtools::document() changes lots of files unexpectedly#

Cause:

  • roxygen output depends on roxygen version and formatting.

Fix:

  • ensure you’re using a recent roxygen2

  • keep roxygen comments stable and avoid rewrapping large blocks unnecessarily

R CMD check fails on vignettes#

Common causes:

  • missing suggested packages (BiocStyle, knitr, rmarkdown)

  • missing Pandoc

Fix:

  • install suggested packages (see setup above)

  • use RStudio’s bundled Pandoc or install Pandoc system-wide

Windows/macOS differences#

Common causes:

  • line ending differences

  • path handling (\\ vs /)

Fix:

  • use file.path() in R code

  • avoid assuming writable directories; use tempdir() in tests/vignettes