Zarr support

.gitignore

@@ -61,3 +61,4 @@ vignettes/data/*.h5ad
 /doc/
 /Meta/
 /data/
+>>>>>>> main

DESCRIPTION

@@ -49,6 +49,7 @@ Suggests:
     knitr,
     processx,
     rhdf5 (>= 2.52.1),
+    Rarr,
     rmarkdown,
     S4Vectors,
     Seurat,

NAMESPACE

@@ -14,10 +14,14 @@ S3method(r_to_py,AbstractAnnData)
 export(AnnData)
 export(AnnDataView)
 export(as_AnnData)
+export(create_zarr)
+export(create_zarr_group)
 export(generate_dataset)
 export(get_generator_types)
 export(read_h5ad)
+export(read_zarr)
 export(write_h5ad)
+export(write_zarr)
 importFrom(Matrix,as.matrix)
 importFrom(Matrix,sparseMatrix)
 importFrom(Matrix,t)

R/AbstractAnnData.R

@@ -287,6 +287,28 @@
       )
     },
     #' @description
+    #' Convert to an [`ZarrAnnData`]
+    #'
+    #' See [as_ZarrAnnData()] for more details on the conversion
+    #'
+    #' @param file See [as_ZarrAnnData()]
+    #' @param compression See [as_ZarrAnnData()]
+    #' @param mode See [as_ZarrAnnData()]
+    #'
+    #' @return An [`ZarrAnnData`] object
+    as_ZarrAnnData = function(
+      file,
+      compression = c("none", "gzip", "lzf"),
+      mode = c("w-", "r", "r+", "a", "w", "x")
+      ) {
+        as_ZarrAnnData(
+          adata = self,
+          file = file,
+          compression = compression,
+          mode = mode
+        )
+    },
+    #' @description
     #' Write the `AnnData` object to an H5AD file
     #'
     #' See [write_h5ad()] for details

R/Rarr_utils.R

@@ -0,0 +1,47 @@
+#' create_zarr_group
+#'
+#' create zarr groups
+#'
+#' @param store the location of (zarr) store
+#' @param name name of the group
+#' @param version zarr version
+#' @export
+create_zarr_group <- function(store, name, version = "v2") {
+  split.name <- strsplit(name, split = "\\/")[[1]]
+  if (length(split.name) > 1) {
+    split.name <- vapply(seq_len(length(split.name)),
+                         function(x) paste(split.name[seq_len(x)], collapse = "/"),
+                         FUN.VALUE = character(1))
+    split.name <- rev(tail(split.name, 2))
+    if (!dir.exists(file.path(store, split.name[2])))
+      create_zarr_group(store = store, name = split.name[2])
+  }
+  dir.create(file.path(store, split.name[1]), showWarnings = FALSE)
+  switch(version,
+         v2 = {
+           write("{\"zarr_format\":2}", file = file.path(store, split.name[1], ".zgroup"))},
+         v3 = {
+           stop("Currently only zarr v2 is supported!")
+         },
+         stop("only zarr v2 is supported. Use version = 'v2'")
+  )
+}
+
+#' create_zarr
+#'
+#' create zarr store
+#'
+#' @param dir the location of zarr store
+#' @param prefix prefix of the zarr store
+#' @param version zarr version
+#' @examples
+#' dir.create(td <- tempfile())
+#' zarr_name <- "test"
+#' create_zarr(dir = td, prefix = "test")
+#' dir.exists(file.path(td, "test.zarr"))
+#' @export
+create_zarr <- function(store, version = "v2") {
+  prefix <- basename(store)
+  dir <- gsub(paste0(prefix, "$"), "", store)
+  create_zarr_group(store = dir, name = prefix, version = version)
+}