stash draft

Former-commit-id: 4364607
Former-commit-id: b8a4e5456b960c63fe2891c6b3661627d9918ee0

Author: HelenaLC

NAMESPACE

@@ -122,6 +122,7 @@ importFrom(SingleCellExperiment,"int_metadata<-")
 importFrom(SingleCellExperiment,SingleCellExperiment)
 importFrom(SingleCellExperiment,int_colData)
 importFrom(SingleCellExperiment,int_metadata)
+importFrom(SpatialExperiment,SpatialExperiment)
 importFrom(SummarizedExperiment,"assay<-")
 importFrom(SummarizedExperiment,"assayNames<-")
 importFrom(SummarizedExperiment,"colData<-")
@@ -130,6 +131,7 @@ importFrom(SummarizedExperiment,colData)
 importFrom(ZarrArray,ZarrArray)
 importFrom(ZarrArray,path)
 importFrom(ZarrArray,type)
+importFrom(anndataR,read_zarr)
 importFrom(arrow,open_dataset)
 importFrom(basilisk,BasiliskEnvironment)
 importFrom(basilisk,basiliskRun)

R/scratch.R

@@ -0,0 +1,33 @@
+#' @importFrom methods as
+#' @importFrom anndataR read_zarr
+#' @importFrom SpatialExperiment SpatialExperiment
+readSDasSPE <- \(x, i=1) { 
+    if (!requireNamespace("SpatialExperiment", quietly=TRUE))
+        stop("install the 'SpatialExperiment' package to use this function.")
+    y <- list.files(file.path(x, "tables"), full.names=TRUE)
+    if (!length(y)) 
+        stop("couldn't find any tables")
+    if (is.character(i)) 
+        i <- match(i, basename(y))
+    sce <- readTable(y[i])
+    colData(sce) <- NULL
+    for (l in setdiff(.LAYERS, "tables")) {
+        y <- list.files(file.path(x, l), full.names=TRUE)
+        y <- y[match(region(sce), basename(y))]
+        if (!is.na(y)) {
+            t <- basename(dirname(y))
+            f <- paste0("read", 
+                toupper(substr(t, 1, 1)), 
+                substr(t, 2, nchar(t)-1))
+            y <- get(f)(y)
+            xy <- centroids(y, "matrix")
+            xy <- xy[, c("x", "y")]
+        }
+    }
+    toSpatialExperiment(sce, spatialCoords=xy)
+}
+
+require(sf, quietly=TRUE)
+x <- file.path("extdata", "blobs.zarr")
+x <- system.file(x, package="SpatialData")
+(spe <- readSDasSPE(x))

R/utils.R

@@ -42,11 +42,13 @@ setMethod("centroids", "ANY", \(x, ...) stop("'centroids' ",
 #' @importFrom Matrix summary
 setMethod("centroids", "LabelArray", \(x, 
     as=c("data.frame", "matrix")) {
-    # TODO: should these be offset by 0.5?
     as <- match.arg(as)
     y <- data(x)
     y <- as(y, "dgCMatrix")
     i <- summary(y)
+    # flip dimensions so that columns=x, rows=y
+    # TODO: should these be offset by 0.5?
+    i[, c(1, 2)] <- i[, c(2, 1)]-0.5
     xy <- tapply(i[, -3], i[[3]], colMeans)
     xy <- do.call(rbind, xy)
     xy <- cbind(xy, as.integer(rownames(xy)))