Adding a utility function to subset RCTD/spacexr object based on spatial spot ids

R/utils.R

@@ -82,3 +82,50 @@ get_class_df <- function(cell_type_names, use_classes = F) {
  }
  return(class_df)
 }
+
+
+#' Subset spatial object to selected barcodes
+#'
+#' Subsets an rctd object based on the input spatial barcode. 
+#' The function subset_rctd subsets the @spatialRNA, @originalSpatialRNA, and @results$weights slots of an RCTD/spacexr object.
+#'
+#' @param rctd_obj An RCTD/spacexr object
+#' @param st_spot_id A vector of scalar character strings that are spatial barcode to keep after subsetting. 
+#' These barcodes should match the spot names in the original spatial object slot of the RCTD/spacexr object used to generate the rctd_obj.
+#'
+#' @return An updated rctd object with rows corresponding only to the barcodes in st_spot_id
+#'
+#' @export
+subset_rctd = function(rctd_obj, st_spot_id){
+ # 1. Report current number of spots.
+ spot_ids_rctd = rownames(rctd_obj@results$weights)
+ message(paste0('Current spatial spot count before subset: ', length(spot_ids_rctd)))
+
+ # 2. Subset input st_spot_id to only those that are in rctd_obj
+ st_spot_id = intersect(st_spot_id, spot_ids_rctd)
+
+ # Throw an error if the subset of spot ids is empty.
+ if(length(st_spot_id) == 0){
+ stop('No spot to keep. Please check input st_spot_id. This should be same as the spot barcodes in spatial object used to generate the RCTD/spacexr object.')
+ }
+
+ # A. subset @spatialRNA slot
+ rctd_obj@spatialRNA@coords = rctd_obj@spatialRNA@coords[st_spot_id, ]
+ rctd_obj@spatialRNA@counts = rctd_obj@spatialRNA@counts[, st_spot_id]
+ rctd_obj@spatialRNA@nUMI = rctd_obj@spatialRNA@nUMI[st_spot_id]
+
+ # B. subset @originalSpatial slot
+ rctd_obj@originalSpatialRNA@coords = rctd_obj@originalSpatialRNA@coords[st_spot_id, ]
+ rctd_obj@originalSpatialRNA@counts = rctd_obj@originalSpatialRNA@counts[, st_spot_id]
+ rctd_obj@originalSpatialRNA@nUMI = rctd_obj@originalSpatialRNA@nUMI[st_spot_id]
+
+ # C. Subset @results$weights
+ rctd_obj@results$weights = rctd_obj@results$weights[st_spot_id, ]
+
+ # 3. Report new number of spots after the subset has been done.
+ spot_ids_rctd_new = rownames(rctd_obj@results$weights)
+ message(paste0('New spatial spot count size after subset: ', length(spot_ids_rctd_new)))
+
+ # Return the resulting subset of the object.
+ return(rctd_obj)
+}