Data Preparation API#

This section is the exhaustive documentation for the R export API:

  • cellucid::cellucid_prepare(...) (primary)

  • cellucid::prepare(...) (alias)

It focuses on:

  • exact input requirements (shapes, types, ordering),

  • file outputs and on-disk formats,

  • edge cases (missing values, huge datasets, weird column types),

  • and troubleshooting (“why did this export fail?”).

Note

If you just want to export something quickly, start with Quick Start (3 Levels) and come back here when you need details.

Recommended reading order

  1. cellucid_prepare() / prepare() Overview

  2. Input Requirements (Global)

  3. Embeddings and Coordinates

  4. obs: Cell Metadata

  5. Gene Expression Matrix (+ var: Gene / Feature Metadata)

  6. Connectivities / KNN Graph (optional)

  7. Vector Fields (Velocity / Displacement) (optional)

  8. Export Directory Format (Specification)

  9. Performance Tuning (Prepare/Export)

  10. Troubleshooting: Prepare/Export