spatialscape init
Write a dataset yaml that doubles as a menu of what the data contains.
The yaml gets one samples: entry per argument. Inside it, fields: already maps the columns that look like spatial domains, cell types and the usual QC metrics (total counts, detected genes, mito percent), and every other column is listed as a comment with its type and levels, so showing one more annotation is uncommenting a line. Optional settings (opening gene, palette, thumbnail, layout) are present as comments. The file builds as written; edit it, then run build.
Usage
bash
spatialscape init <PATHS>... [OPTIONS]Arguments
| Argument | Type | Default | Description |
|---|---|---|---|
PATHS | text | required | What to describe: R objects (.rds / .rda holding a SpatialExperiment, SingleCellExperiment or Seurat object), globs of sample files such as 'data/*/adata.h5ad' (quoted, so the shell does not expand them), and results tables of differential expression tests (.csv / .tsv / .parquet, one row per gene). One samples: entry per object or glob, one comparisons: entry per table. |
Options
| Option | Type | Default | Description |
|---|---|---|---|
-o, --out | path | — | Where to write the yaml. Default: <id>.yaml in the current folder. |
--id | text | — | Dataset id: used in ?d=<id> and as the bundle folder name. Default: the object's file name, or the folder a glob starts in. |
--name | text | — | Human-readable dataset name. Default: the id, prettified. |
--platform | text | — | Platform of the spatial samples: visium, visium_hd, xenium, merfish or other. Default: guessed from the columns (array_row / array_col mean Visium when the grid fits one Visium array or the spots split into capture areas of Visium size, Visium HD when the grid is larger; Xenium's cell metrics mean Xenium), else visium; the yaml says which. Objects and files without spatial coordinates become snrnaseq embeddings regardless. |
--table | text | — | Table key inside a SpatialData store. |
Examples
A SpatialExperiment saved from R (one sample per sample_id)
bash
spatialscape init analysis/spe_visium.rds --id dlpfc --name "Human DLPFC"Xenium donors in sibling folders
bash
spatialscape init "xenium/*/adata.zarr" --platform xenium --id amygdala --name "Human amygdala"A spatial object and the snRNA-seq reference behind its labels, one dataset
bash
spatialscape init analysis/spe_visium.rds analysis/sce_snrnaseq.rds --id dlpfc