Write cells as a SpatialData Zarr store

Writes a data.frame of cells as the cell table of a SpatialData Zarr store (an AnnData table under tables/, in Zarr v3), which spicy() reads a block of rows at a time and spatialdataR's readSpatialData() reads as a SpatialData object. The coordinates become the obsm array "spatial", the other columns the table's obs (factors as categorical columns), and the image column the table's region key (always a categorical column, its categories the levels of a factor, else the images in order of first appearance). A table with one row per image can be added as a second table. Each column is written in chunks of 2^20 rows compressed with zstd, one chunk at a time, so writing needs little memory beyond that of cells, however many cells it has.

Usage

writeCellStore(
  cells,
  path,
  imageID = "imageID",
  spatialCoords = c("x", "y"),
  tableKey = "table",
  imageInfo = NULL,
  infoKey = "images"
)

Arguments

cells

A data.frame with one row per cell. Its columns are factors, character, integer, double or logical vectors.

path

The directory of the store (replaced if it exists).

imageID, spatialCoords

The column of the image and the two columns of the coordinates.

tableKey

The name of the cell table.

imageInfo

Optional: a data.frame with one row per image (row names: the image IDs), written as the table infoKey.

infoKey

The name of the per-image table.

Value

path, invisibly.

Examples

cells <- data.frame(imageID = factor(rep(c("a", "b"), each = 50)), cellType = factor(rep(c("T", "B"), 50)),
                    x = runif(100, 0, 100), y = runif(100, 0, 100))
if (requireNamespace("Rarr", quietly = TRUE)) {
  path <- writeCellStore(cells, tempfile(fileext = ".zarr"))
  list.files(file.path(path, "tables"))
}
#> [1] "table"     "zarr.json"