From 83dd41f475d6b7f678d4d9baf21902a41c6aad31 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Tue, 18 Jun 2024 12:43:43 -0400
Subject: [PATCH] WIP: use pizzarr and anndataR

---
 R/data_to_zarr.R | 53 +++---------------------------------------------
 1 file changed, 3 insertions(+), 50 deletions(-)

diff --git a/R/data_to_zarr.R b/R/data_to_zarr.R
index 8fa9a3c..dff87ac 100644
--- a/R/data_to_zarr.R
+++ b/R/data_to_zarr.R
@@ -11,56 +11,9 @@
 #' obj <- get_seurat_obj()
 #' seurat_to_anndata_zarr(obj, out_path = "data/seurat.zarr", assay = "RNA")
 seurat_to_anndata_zarr <- function(seurat_obj, out_path, assay) {
-  if(!requireNamespace("SeuratDisk", quietly = TRUE)) {
-    stop("Install 'SeuratDisk' to enable conversion of Seurat objects to AnnData objects.")
-  }
-
-  h5seurat_path <- paste0(out_path, ".h5Seurat")
-  h5ad_path <- paste0(out_path, ".h5ad")
-
-  # Convert factor columns to string/numeric.
-  seurat_obj@meta.data <- varhandle::unfactor(seurat_obj@meta.data)
-
-  SeuratDisk::SaveH5Seurat(seurat_obj, filename = h5seurat_path, overwrite = TRUE)
-  SeuratDisk::Convert(h5seurat_path, dest = "h5ad", overwrite = TRUE, assay = assay)
-
-  # Use basilisk
-  proc <- basilisk::basiliskStart(py_env)
-  on.exit(basilisk::basiliskStop(proc))
-
-  success <- basilisk::basiliskRun(proc, function(h5ad_path, out_path) {
-    anndata <- reticulate::import("anndata")
-    zarr <- reticulate::import("zarr")
-
-    adata <- anndata$read_h5ad(h5ad_path)
-
-    cleanup_colnames <- function(df) {
-      # Reference: https://github.com/theislab/scvelo/issues/255#issuecomment-739995301
-      new_colnames <- colnames(df)
-      new_colnames[new_colnames == "_index"] <- "features"
-      return(new_colnames)
-    }
-
-    noop <- function(cond) { }
-
-    tryCatch({
-      colnames(adata$var) <- cleanup_colnames(adata$var)
-    }, error = noop)
-
-    # Reconstruct, omitting raw and uns.
-    adata <- anndata$AnnData(
-      X = adata$X,
-      obs = as.data.frame(adata$obs),
-      var = as.data.frame(adata$var),
-      obsm = adata$obsm,
-      varm = adata$varm
-    )
-
-    adata$write_zarr(out_path)
-
-    return(TRUE)
-  }, h5ad_path = h5ad_path, out_path = out_path)
-  return(success)
+  sce <- Seurat::as.SingleCellExperiment(seurat_obj)
+  store <- pizzarr::DirectoryStore$new(out_path)
+  anndataR::from_SingleCellExperiment(sce, "ZarrAnnData", store = store)
 }
 
 #' Save a SingleCellExperiment to an AnnData-Zarr store.