Merge branch 'dev' into dev2

NAMESPACE

@@ -320,6 +320,7 @@ exportMethods("prov<-")
 exportMethods("spatUnit<-")
 exportMethods(activeFeatType)
 exportMethods(activeSpatUnit)
+exportMethods(as.matrix)
 exportMethods(as.points)
 exportMethods(as.polygons)
 exportMethods(as.sf)

NEWS.md

@@ -14,6 +14,7 @@
 
 ## new
 - `as()` conversion from `giottoLargeImage` to `array`
+- `as.matrix()` method for `spatLocsObj()`
 
 
 # GiottoClass 0.3.0 (2024/05/13)

R/methods-coerce.R

@@ -22,6 +22,19 @@ NULL
 #' data.table::as.data.table(g)
 NULL
 
+#' @title Coerce to matrix
+#' @name as.matrix
+#' @description Coerce to matrix
+#' @param x object to coerce
+#' @param id_rownames logical. Retain the spatial IDs as the rownames
+#' @param \dots additional params to pass (none implemented)
+#' @examples
+#' sl <- GiottoData::loadSubObjectMini("spatLocsObj")
+#' m <- as.matrix(sl)
+#' @family As coercion functions
+#' @returns matrix
+NULL
+
 
 #' @title Coerce to SpatVector polygons
 #' @name as.polygons
@@ -107,6 +120,30 @@ as.data.table.giottoPoints <- function(x, ...) {
 
 
 
+# to matrix ####
+
+
+#' @rdname as.matrix
+#' @export
+setMethod("as.matrix", signature("spatLocsObj"), function(
+        x, id_rownames = TRUE, ...) {
+
+    x <- x[] # drop to DT
+    spat_cols <- c("sdimx", "sdimy", "sdimz")
+    spat_cols <- spat_cols %in% colnames(x)
+
+    m <- x[, spat_cols, with = FALSE] %>%
+        as.matrix()
+
+    if (id_rownames) {
+        rownames(m) <- x$cell_ID
+    }
+    return(m)
+})
+
+
+
+
 # image types ####
 
 methods::setAs("giottoLargeImage", "giottoImage", function(from) {
@@ -137,6 +174,8 @@ methods::setAs("giottoLargeImage", "giottoImage", function(from) {
     return(mImg)
 })
 
+# TODO redo this as `as.array`. 
+# Careful: There are already usages of this `as()` method in the code
 methods::setAs("giottoLargeImage", "array", function(from) {
     .spatraster_sample_values(
         raster_object = from,