Zarr support

.gitignore

@@ -60,4 +60,4 @@ rsconnect/
 vignettes/data/*.h5ad
 /doc/
 /Meta/
-/data/
+/data/

DESCRIPTION

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

NAMESPACE

@@ -14,10 +14,15 @@ 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(is_zarr_empty)
 export(read_h5ad)
+export(read_zarr)
 export(write_h5ad)
+export(write_zarr)
 importFrom(Matrix,as.matrix)
 importFrom(Matrix,sparseMatrix)
 importFrom(Matrix,t)
@@ -35,3 +40,4 @@ importFrom(reticulate,r_to_py)
 importFrom(rlang,`%||%`)
 importFrom(rlang,caller_env)
 importFrom(stats,setNames)
+importFrom(utils,tail)

R/AbstractAnnData.R

@@ -287,6 +287,28 @@ AbstractAnnData <- R6::R6Class(
       )
     },
     #' @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"),
+      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
@@ -302,6 +324,23 @@ AbstractAnnData <- R6::R6Class(
       mode = c("w-", "r", "r+", "a", "w", "x")
     ) {
       write_h5ad(object = self, path, compression = compression, mode = mode)
+    },
+    #' @description
+    #' Write the `AnnData` object to an H5AD file
+    #'
+    #' See [write_zarr()] for details
+    #'
+    #' @param path See [write_zarr()]
+    #' @param compression See [write_zarr()]
+    #' @param mode See [write_zarr()]
+    #'
+    #' @return `path` invisibly
+    write_zarr = function(
+      path,
+      compression = c("none", "gzip"),
+      mode = c("w-", "r", "r+", "a", "w", "x")
+    ) {
+      write_zarr(object = self, path, compression = compression, mode = mode)
     }
   ),
   private = list(

R/Rarr_utils.R

@@ -0,0 +1,75 @@
+#' create_zarr_group
+#'
+#' create zarr groups
+#'
+#' @param store the location of (zarr) store
+#' @param name name of the group
+#' @param version zarr version
+#' @importFrom utils tail
+#' @examples
+#' store <- tempfile(fileext = ".zarr")
+#' create_zarr(store)
+#' create_zarr_group(store, "gp")
+#' @export
+#' @return `NULL`
+create_zarr_group <- function(store, name, version = "v2") {
+  split.name <- strsplit(name, split = "\\/")[[1]]
+  if (length(split.name) > 1) {
+    split.name <- vapply(
+      seq_along(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 store the location of zarr store
+#' @param version zarr version
+#' @examples
+#' store <- tempfile(fileext = ".zarr")
+#' create_zarr(store)
+#' @export
+#' @return `NULL`
+create_zarr <- function(store, version = "v2") {
+  prefix <- basename(store)
+  dir <- gsub(paste0(prefix, "$"), "", store)
+  create_zarr_group(store = dir, name = prefix, version = version)
+}
+
+#' create_zarr
+#'
+#' create zarr store
+#'
+#' @param store the location of zarr store
+#' @examples
+#' store <- tempfile(fileext = ".zarr")
+#' create_zarr(store)
+#' is_zarr_empty(store)
+#' @export
+#' @return returns TRUE if zarr store is not empty
+is_zarr_empty <- function(store) {
+  files <- list.files(store, recursive = FALSE, full.names = FALSE)
+  all(files %in% c(".zarray", ".zattrs", ".zgroup"))
+}