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The main goal of this R package is to enable configuring Vitessce visualizations using R syntax.

We also aim to simplify the data conversion process by providing dataset wrapper classes that automatically convert common single-cell data structures to file formats supported by Vitessce.

Our effort to develop converters for R formats remains ongoing. However, we provide a guide for R developers to write data conversion functions to support any type of R single-cell data structure (or to improve conversion for already-supported data structures).

The following vignettes in the "Examples with Local Data" section demonstrate how the dataset wrapper classes can be used with single-cell datasets stored on your local machine.

Zarr via Reticulate via Basilisk

Due to a lack of native R support for Zarr, the R dataset conversion functions currently depend on a Python environment.

We currently use basilisk and reticulate to write to Zarr stores via the zarr Python package.

Zarr natively

Subscribe to the Zarr in R issue for future updates about native Zarr support that would avoid the need for the Python environment.