move functions. allow writing anndata objects to file

R/read_h5ad.R

@@ -0,0 +1,33 @@
+#' Read H5AD
+#'
+#' Read data from a H5AD file
+#'
+#' @param path Path to the H5AD file to read
+#' @param to The type of object to return. Must be one of: "SingleCellExperiment",
+#'   "Seurat", "HDF5AnnData", "InMemoryAnnData"
+#'
+#' @return The object specified by `to`
+#' @export
+#'
+#' @examples
+#' h5ad_file <- system.file("extdata", "example.h5ad", package = "anndataR")
+#' # Read the H5AD as a SingleCellExperiment object
+#' if (requireNamespace("SingleCellExperiment", quietly = TRUE)) {
+#'   sce <- read_h5ad(h5ad_file, to = "SingleCellExperiment")
+#' }
+#' # Read the H5AD as a Seurat object
+#' if (requireNamespace("SeuratObject", quietly = TRUE)) {
+#'   seurat <- read_h5ad(h5ad_file, to = "Seurat")
+#' }
+read_h5ad <- function(path, to = c("SingleCellExperiment", "Seurat", "HDF5AnnData", "InMemoryAnnData")) {
+  to <- match.arg(to)
+
+  adata <- HDF5AnnData$new(path)
+
+  switch(to,
+    "SingleCellExperiment" = to_SingleCellExperiment(adata),
+    "Seurat" = to_Seurat(adata),
+    "HDF5AnnData" = adata,
+    "InMemoryAnnData" = to_InMemoryAnnData(adata)
+  )
+}

R/HDF5-read.R → R/read_h5ad_helpers.R

@@ -430,37 +430,3 @@ read_h5ad_collection <- function(file, name, column_order) {
   }
   columns
 }
-
-#' Read H5AD
-#'
-#' Read data from a H5AD file
-#'
-#' @param path Path to the H5AD file to read
-#' @param to The type of object to return. Must be one of: "SingleCellExperiment",
-#'   "Seurat", "HDF5AnnData", "InMemoryAnnData"
-#'
-#' @return The object specified by `to`
-#' @export
-#'
-#' @examples
-#' h5ad_file <- system.file("extdata", "example.h5ad", package = "anndataR")
-#' # Read the H5AD as a SingleCellExperiment object
-#' if (requireNamespace("SingleCellExperiment", quietly = TRUE)) {
-#'   sce <- read_h5ad(h5ad_file, to = "SingleCellExperiment")
-#' }
-#' # Read the H5AD as a Seurat object
-#' if (requireNamespace("SeuratObject", quietly = TRUE)) {
-#'   seurat <- read_h5ad(h5ad_file, to = "Seurat")
-#' }
-read_h5ad <- function(path, to = c("SingleCellExperiment", "Seurat", "HDF5AnnData", "InMemoryAnnData")) {
-  to <- match.arg(to)
-
-  adata <- HDF5AnnData$new(path)
-
-  switch(to,
-    "SingleCellExperiment" = to_SingleCellExperiment(adata),
-    "Seurat" = to_Seurat(adata),
-    "HDF5AnnData" = adata,
-    "InMemoryAnnData" = to_InMemoryAnnData(adata)
-  )
-}

R/write_h5ad.R

@@ -0,0 +1,83 @@
+#' Write H5AD
+#'
+#' Write an H5AD file
+#'
+#' @param object The object to write, either a "SingleCellExperiment" or a
+#' "Seurat" object
+#' @param path Path of the file to write to
+#'
+#' @return `path` invisibly
+#' @export
+#'
+#' @examples
+#' adata <- AnnData(
+#'   X = matrix(1:15, 3L, 5L),
+#'   layers = list(
+#'     A = matrix(15:1, 3L, 5L),
+#'     B = matrix(letters[1:15], 3L, 5L)
+#'   ),
+#'   obs = data.frame(cell = 1:3),
+#'   var = data.frame(gene = 1:5),
+#'   obs_names = LETTERS[1:3],
+#'   var_names = letters[1:5]
+#' )
+#' h5ad_file <- tempfile(fileext = ".h5ad")
+#' write_h5ad(adata, h5ad_file)
+#'
+#' # Write a SingleCellExperiment as a H5AD
+#' h5ad_file <- tempfile(fileext = ".h5ad")
+#' if (requireNamespace("SingleCellExperiment", quietly = TRUE)) {
+#'   sce <- SingleCellExperiment(
+#'    assays = list(
+#'      counts = matrix(1:15, 3L, 5L),
+#'      A = matrix(15:1, 3L, 5L),
+#'      B = matrix(letters[1:15], 3L, 5L)
+#'    ),
+#'    rowData = data.frame(gene = 1:5),
+#'    colData = data.frame(cell = 1:3),
+#'   )
+#'   write_h5ad(sce, h5ad_file)
+#' }
+#'
+#' # Write a Seurat as a H5AD
+#' h5ad_file <- tempfile(fileext = ".h5ad")
+#' if (requireNamespace("SeuratObject", quietly = TRUE)) {
+#'   counts <- matrix(1:15, 3L, 5L)
+#'   dimnames(counts) <- list(
+#'     letters[1:3],
+#'     LETTERS[1:5]
+#'   )
+#'   gene.metadata <- data.frame(
+#'     row.names = LETTERS[1:5],
+#'     gene = 1:5
+#'   )
+#'   obj <- SeuratObject::CreateSeuratObject(counts, meta.data = gene.metadata)
+#'   cell.metadata <- data.frame(
+#'     row.names = letters[1:3],
+#'     cell = 1:3
+#'   )
+#'   obj <- SeuratObject::AddMetaData(obj, cell.metadata)
+#'
+#'   write_h5ad(obj, h5ad_file)
+#' }
+write_h5ad <- function(object, path) {
+  if (inherits(object, "SingleCellExperiment")) {
+    from_SingleCellExperiment(
+      object,
+      output_class = "HDF5AnnData",
+      file = path
+    )
+  } else if (inherits(object, "Seurat")) {
+    from_Seurat(
+      object,
+      output_class = "HDF5AnnData",
+      file = path
+    )
+  } else if (inherits(object, "AbstractAnnData")) {
+    to_HDF5AnnData(object, path)
+  } else {
+    stop("Unable to write object of class: ", class(object))
+  }
+
+  invisible(path)
+}

R/HDF5-write.R → R/write_h5ad_helpers.R

@@ -468,88 +468,4 @@ hdf5_path_exists <- function(file, target_path) {
   paths <- gsub("//", "/", paths) # Remove double slash for root paths
 
   target_path %in% paths
-}
-
-#' Write H5AD
-#'
-#' Write an H5AD file
-#'
-#' @param object The object to write, either a "SingleCellExperiment" or a
-#' "Seurat" object
-#' @param path Path of the file to write to
-#'
-#' @return `path` invisibly
-#' @export
-#'
-#' @examples
-#' adata <- AnnData(
-#'   X = matrix(1:15, 3L, 5L),
-#'   layers = list(
-#'     A = matrix(15:1, 3L, 5L),
-#'     B = matrix(letters[1:15], 3L, 5L)
-#'   ),
-#'   obs = data.frame(cell = 1:3),
-#'   var = data.frame(gene = 1:5),
-#'   obs_names = LETTERS[1:3],
-#'   var_names = letters[1:5]
-#' )
-#' h5ad_file <- tempfile(fileext = ".h5ad")
-#' write_h5ad(adata, h5ad_file)
-#'
-#' # Write a SingleCellExperiment as a H5AD
-#' h5ad_file <- tempfile(fileext = ".h5ad")
-#' if (requireNamespace("SingleCellExperiment", quietly = TRUE)) {
-#'   sce <- SingleCellExperiment(
-#'    assays = list(
-#'      counts = matrix(1:15, 3L, 5L),
-#'      A = matrix(15:1, 3L, 5L),
-#'      B = matrix(letters[1:15], 3L, 5L)
-#'    ),
-#'    rowData = data.frame(gene = 1:5),
-#'    colData = data.frame(cell = 1:3),
-#'   )
-#'   write_h5ad(sce, h5ad_file)
-#' }
-#'
-#' # Write a Seurat as a H5AD
-#' h5ad_file <- tempfile(fileext = ".h5ad")
-#' if (requireNamespace("SeuratObject", quietly = TRUE)) {
-#'   counts <- matrix(1:15, 3L, 5L)
-#'   dimnames(counts) <- list(
-#'     letters[1:3],
-#'     LETTERS[1:5]
-#'   )
-#'   gene.metadata <- data.frame(
-#'     row.names = LETTERS[1:5],
-#'     gene = 1:5
-#'   )
-#'   obj <- SeuratObject::CreateSeuratObject(counts, meta.data = gene.metadata)
-#'   cell.metadata <- data.frame(
-#'     row.names = letters[1:3],
-#'     cell = 1:3
-#'   )
-#'   obj <- SeuratObject::AddMetaData(obj, cell.metadata)
-#'
-#'   write_h5ad(obj, h5ad_file)
-#' }
-write_h5ad <- function(object, path) {
-  if (inherits(object, "SingleCellExperiment")) {
-    from_SingleCellExperiment(
-      object,
-      output_class = "HDF5AnnData",
-      file = path
-    )
-  } else if (inherits(object, "Seurat")) {
-    from_Seurat(
-      object,
-      output_class = "HDF5AnnData",
-      file = path
-    )
-  } else {
-    (
-      stop("Unable to write object of class: ", class(object))
-    )
-  }
-
-  invisible(path)
-}
+}