Refactoring

DESCRIPTION

@@ -24,7 +24,7 @@ LazyData: false
 Language: en-US
 StagedInstall: no
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Imports:
     Matrix,

NAMESPACE

@@ -3,13 +3,16 @@
 export(get_giotto_obj)
 export(get_sce_obj)
 export(get_seurat_obj)
+export(get_seurat_v5_obj)
 export(get_spe_obj)
 export(giotto_to_anndata_zarr)
 export(obj_list)
 export(sce_to_anndata_zarr)
 export(seurat_to_anndata_zarr)
 export(spe_to_anndata_zarr)
 export(spe_to_ome_zarr)
+import(Seurat)
+import(SeuratObject)
 importFrom(SingleCellExperiment,"reducedDims<-")
 importFrom(SingleCellExperiment,int_colData)
 importFrom(SingleCellExperiment,reducedDims)

R/data_to_zarr.R → R/bioc_to_zarr.R

@@ -1,34 +1,3 @@
-
-#' Save a Seurat object to an AnnData-Zarr store.
-#'
-#' @param seurat_obj The object to save.
-#' @param out_path A path to the output Zarr store.
-#' @param assay The name of the assay to save.
-#' @return TRUE if the conversion succeeds.
-#'
-#' @export
-#' @examples
-#' obj <- get_seurat_obj()
-#' seurat_to_anndata_zarr(obj, out_path = "data/seurat.zarr")
-seurat_to_anndata_zarr <- function(seurat_obj, out_path) {
-  sce <- Seurat::as.SingleCellExperiment(seurat_obj)
-  store <- pizzarr::DirectoryStore$new(out_path)
-  anndataR::from_SingleCellExperiment(sce, "ZarrAnnData", store = store)
-}
-
-test_conversion <- function(num_workers = 8) {
-  options(
-    pizzarr.parallel_read_enabled = TRUE,
-    pizzarr.parallel_write_enabled = TRUE
-  )
-  doParallel::registerDoParallel(num_workers)
-
-  obj <- get_seurat_obj()
-  seurat_to_anndata_zarr(obj, "test.zarr")
-
-  doParallel::stopImplicitCluster()
-}
-
 #' Save a SingleCellExperiment to an AnnData-Zarr store.
 #'
 #' @param sce_obj The object to save.
@@ -48,20 +17,10 @@ sce_to_anndata_zarr <- function(sce_obj, out_path) {
     # Reference: https://github.com/theislab/zellkonverter/blob/e1e95b1/R/SCE2AnnData.R#L159
     colnames(reducedDims(sce_obj)[[obsm_key]]) <- NULL
   }
-
-  # Use basilisk
-  proc <- basilisk::basiliskStart(py_env)
-  on.exit(basilisk::basiliskStop(proc))
-
-  success <- basilisk::basiliskRun(proc, function(sce_obj, out_path) {
-    anndata <- reticulate::import("anndata")
-    zarr <- reticulate::import("zarr")
-
-    adata <- zellkonverter::SCE2AnnData(sce_obj)
-    adata$write_zarr(out_path)
-    return(TRUE)
-  }, sce_obj = sce_obj, out_path = out_path)
-  return(success)
+
+  store <- pizzarr::DirectoryStore$new(out_path)
+  anndataR::from_SingleCellExperiment(sce_obj, "ZarrAnnData", store = store)
+  return(TRUE)
 }
 
 #' Save a SpatialExperiment to an AnnData-Zarr store.
@@ -166,70 +125,3 @@ spe_to_ome_zarr <- function(spe_obj, sample_id, image_id, out_path) {
   }, img_arr = img_arr, sample_id = sample_id, image_id = image_id, out_path = out_path)
   return(success)
 }
-
-#' Save a Giotto object to an AnnData-Zarr store
-#'
-#' @param giotto_obj The object to save.
-#' @param out_path A path to the output Zarr store.
-#' @param X_slot The name of the slot in the Giotto object to use for adata.X
-#' @return TRUE if the conversion succeeds.
-#'
-#' @export
-#' @examples
-#' obj <- get_giotto_obj()
-#' giotto_to_anndata_zarr(obj, "data/giotto.zarr")
-#' @importFrom methods slot
-giotto_to_anndata_zarr <- function(giotto_obj, out_path, X_slot = "raw_exprs") {
-
-  # Use basilisk
-  proc <- basilisk::basiliskStart(py_env)
-  on.exit(basilisk::basiliskStop(proc))
-
-  success <- basilisk::basiliskRun(proc, function(giotto_obj, out_path, X_slot) {
-    anndata <- reticulate::import("anndata")
-    zarr <- reticulate::import("zarr")
-
-    # Reference: https://github.com/theislab/zellkonverter/blob/master/R/SCE2AnnData.R#L237
-    make_numpy_friendly <- function(x, transpose = TRUE) {
-      if (transpose) {
-        x <- Matrix::t(x)
-      }
-      if (DelayedArray::is_sparse(x)) {
-        methods::as(x, "dgCMatrix")
-      } else {
-        as.matrix(x)
-      }
-    }
-
-    X <- make_numpy_friendly(slot(giotto_obj, X_slot))
-    obs <- slot(giotto_obj, "cell_metadata")
-    var <- slot(giotto_obj, "gene_metadata")
-
-    adata <- anndata$AnnData(X = X, obs = obs, var = var)
-
-    obsm <- list()
-
-    if(!is.null(slot(giotto_obj, "spatial_locs"))) {
-      spatial_locs <- slot(giotto_obj, "spatial_locs")
-      obsm[['spatial']] <- t(as.matrix(spatial_locs[, c("sdimx", "sdimy")]))
-    }
-
-    if(!is.null(slot(giotto_obj, "dimension_reduction"))) {
-      dim_reducs <- slot(giotto_obj, "dimension_reduction")$cells
-      for(dim_reduc_name in names(dim_reducs)) {
-        dim_reduc_coords <- dim_reducs[[dim_reduc_name]][[dim_reduc_name]]$coordinates
-        obsm[[dim_reduc_name]] <- t(as.matrix(dim_reduc_coords))
-      }
-    }
-
-    if(length(obsm) > 0) {
-      # TODO make_numpy_friendly is outside scope
-      obsm <- lapply(obsm, make_numpy_friendly)
-      adata$obsm <- obsm
-    }
-
-    adata$write_zarr(out_path)
-    return(TRUE)
-  }, giotto_obj = giotto_obj, out_path = out_path, X_slot = X_slot)
-  return(success)
-}

R/giotto_to_bioc.R

@@ -0,0 +1,3 @@
+giotto_to_spe <- function(gio) {
+  return(GiottoClass::giottoToSpatialExperiment(gio))
+}

R/mock_objects.R

@@ -1,5 +1,16 @@
-library(Seurat)
-library(SeuratObject)
+#' Get a Seurat v5 object for tests and examples.
+#' @return The object.
+#' @keywords internal
+#' @export
+#' @examples
+#' obj <- get_seurat_v5_obj()
+#' @import Seurat
+#' @import SeuratObject
+get_seurat_v5_obj <- function() {
+  SeuratData::InstallData("pbmcsca")
+  obj <- SeuratData::LoadData("pbmcsca")
+  return(obj)
+}
 
 #' Create a mock Seurat object for tests and examples.
 #' @return The object.
@@ -12,10 +23,6 @@ get_seurat_obj <- function() {
   if(!requireNamespace("Seurat", quietly = TRUE)) {
     stop("Install 'Seurat' to enable creation of Seurat objects.")
   }
-
-  SeuratData::InstallData("pbmcsca")
-  obj <- SeuratData::LoadData("pbmcsca")
-  return(obj)
 
   ncells <- 100
   u <- matrix(rpois(20000, 5), ncol=ncells)

R/seurat_to_bioc.R

@@ -0,0 +1,62 @@
+seurat_to_sce <- function(seu) {
+  sce <- Seurat::as.SingleCellExperiment(seu)
+  return(sce)
+}
+
+seurat_to_spe <- function(seu, sample_id = NA, img_id = NA) {
+  # Reference: https://github.com/drighelli/SpatialExperiment/issues/115
+  sce <- seurat_to_sce(seu)
+
+  if(is.na(sample_id)) {
+    sample_id <- "sample0"
+  }
+
+  if(length(object@images) >= 1) {
+
+    if(is.na(img_id)) {
+      img_id <- names(object@images)[1]
+    }
+
+    ## Extract spatial coordinates
+    if("VisiumV2" %in% class(seu@images[[img_id]])) {
+      spatialCoords <- as.matrix(
+        seu@images[[img_id]]@boundaries$centroids@coords
+      )
+    } else {
+      spatialCoords <- as.matrix(
+        seu@images[[img_id]]@coordinates[, c("imagecol", "imagerow")]
+      )
+    }
+
+
+    ## Extract and process image data
+    img <- SpatialExperiment::SpatialImage(
+      x = as.raster(seu@images[[img_id]]@image)
+    )
+
+    imgData <- S4Vectors::DataFrame(
+      sample_id = sample_id,
+      image_id = img_id,
+      data = I(list(img)),
+      scaleFactor = seu@images[[img_id]]@scale.factors$lowres
+    )
+  }
+
+  # Convert to SpatialExperiment
+  spe <- SpatialExperiment::SpatialExperiment(
+    assays = SummarizedExperiment::assays(sce),
+    rowData = SingleCellExperiment::rowData(sce),
+    colData = SingleCellExperiment::colData(sce),
+    metadata = S4Vectors::metadata(sce),
+    reducedDims = SingleCellExperiment::reducedDims(sce),
+    altExps = SingleCellExperiment::altExps(sce),
+    sample_id = sample_id,
+    spatialCoords = spatialCoords,
+    imgData = imgData
+  )
+  # indicate all spots are on the tissue
+  spe$in_tissue <- 1
+  spe$sample_id <- sample_id
+  # Return Spatial Experiment object
+  return(spe)
+}