vitessceR

vitessceR copied to clipboard

Describe the bug using vc$export("[out dir]"), None of the cells.json, cell-sets.json, and clusters.json are found in the output directory. Only folders with vitessce config datasets are found.

To Reproduce Tested with the example (https://vitessce.github.io/vitessceR/articles/seuratdata.html) as well as own data. Both do not work. Following the procedure here: https://vitessce.github.io/vitessceR/articles/export_files.html?q=export#export-files-for-serving-locally

Expected behavior cells.json, cell-sets.json, and clusters.json should appear in the output folder

Screenshots

Environment:

• Release or git hash: VitessceR_0.99.0
• Operating system: Windows 10
• R version: 4.2.1
• RStudio version: 2022.07.2+576

It's possible there's a bug. Without your code specifically it's tough to say (it sounds like you customized the exporting demo) - have you confirmed with the with_config = TRUE argument, you still get this behavior? I also think the config would be at the root, probably output, and not in this file directory.

I think the "Export data to static files" page is out of date. Seurat objects were previously converted to JSON format, but are now converted to Zarr, as Zarr is more efficient (supports compression etc).