read AnnData-zarr tables directly

R/read.R

@@ -131,22 +131,24 @@ readShape <- function(x, ...) {
     proc <- basiliskStart(.env)
     on.exit(basiliskStop(proc))
     basiliskRun(proc, x=x, \(x) {
-        # read in 'SpatialData' from .zarr store
-        sd <- import("spatialdata")
-        zs <- sd$read_zarr(x)
-        # return (named) list of SCEs
-        names(ts) <- ts <- names(zs$tables$data)
-        lapply(ts, \(z) {
-            se <- AnnData2SCE(zs$tables[z])
-            nm <- "spatialdata_attrs"
-            md <- metadata(se)[[nm]]
-            int_metadata(se)[[nm]] <- md
-            metadata(se)[[nm]] <- NULL
-            se
-        }) 
+      # read in 'AnnData' tables from .zarr store
+      sd <- import("anndata")
+      za <- import("zarr")
+      # return (named) list of SCEs
+      names(ts) <- ts <- list.dirs(file.path(x,"tables/"), 
+                                   recursive = FALSE, 
+                                   full.names = FALSE)
+      lapply(ts, \(z) {
+        zs <- sd$read_zarr(file.path(x, "tables", z))
+        se <- AnnData2SCE(zs)
+        nm <- "spatialdata_attrs"
+        md <- metadata(se)[[nm]]
+        int_metadata(se)[[nm]] <- md
+        metadata(se)[[nm]] <- NULL
+        se
+      }) 
     })
 }
-
 .readTable_anndataR <- function(x) {
     if (!requireNamespace('anndataR', quietly=TRUE)) {
         stop("To use this function, install the 'anndataR' package via\n",