Merge pull request #27 from boyiguo1/v1.1.2

Add Example to make_escheR Manual

R/make_escheR.R

@@ -32,10 +32,23 @@
 #'
 #' @examples
 #' library(STexampleData)
-#'
+#' # SpatialExperiment Object
 #' spe <- Visium_humanDLPFC()
-#'
 #' make_escheR(spe)
+#'
+#' # SingleCellExperiment Object
+#' sce <- SingleCellExperiment(counts(spe))
+#' reducedDims(sce) <- list(
+#'    # Example embedding
+#'     EG = matrix(seq.int(1, ncol(spe)*2), ncol = 2)
+#'     )
+#' make_escheR(sce, dimred = "EG")
+#'
+#' # data.frame Object
+#' x <- spatialCoords(spe)[,1]
+#' y <- spatialCoords(spe)[,2]
+#' df <- colData(spe) |> data.frame()
+#' make_escheR(object = df, .x = x , .y = y)
 make_escheR <- function(object, spot_size = 2, ...) {
   UseMethod("make_escheR", object)
 }
@@ -80,8 +93,8 @@ make_escheR.SingleCellExperiment <- function(
          " is not found in reducedDim(object).")
 
 
-  if(ncol(reducedDim(sce, dimred)) <= 2)
-    stop("reducedDim(object, ", dimred, " ) must have more than 2 columns.")
+  if(ncol(reducedDim(sce, dimred)) < 2)
+    stop("reducedDim(object, ", dimred, " ) must have at least 2 columns.")
 
   # TODO (Medium): How about dimension reduction assays?
   coord_df <- reducedDim(sce, dimred)[ , c(1,2), drop = FALSE]