fix :: calls

Author: HelenaLC

R/plotFrame.R

@@ -93,14 +93,14 @@ NULL
 setMethod("plotShape", "SpatialData", \(x, i=1, j=1, assay=1, ...) {
     if (is.numeric(i)) i <- shapeNames(x)[i]
     y <- shape(x, i)
-    y <- SpatialData::transform(y, j)
+    y <- spatialdataR::transform(y, j)
     .plot(x, y, assay=assay, i=i, ...)
 })
 #' @export
 #' @rdname plotFrame
 setMethod("plotPoint", "SpatialData", \(x, i=1, j=1, ...) {
     if (is.numeric(i)) i <- pointNames(x)[i]
     y <- point(x, i)
-    y <- SpatialData::transform(y, j)
+    y <- spatialdataR::transform(y, j)
     .plot(x, y, i=i, ...)
 })

R/plotLabel.R

@@ -75,7 +75,7 @@ setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL,
         t <- table(x, hasTable(x, i, name=TRUE))
         ik <- .instance_key(t)
         # TODO: search ik in both internal and regular colData for now
-        # thus perhaps update, SpatialData::valTable instead
+        # thus perhaps update, spatialdataR::valTable instead
         # idx <- match(df$z, int_colData(t)[[ik]])
         if(ik %in% names(int_colData(t))){
           coldata <- int_colData(t)[[ik]]

vignettes/SpatialData.plot.Rmd

@@ -162,8 +162,8 @@ pa <- get_demo_SDdata("merfish")
 (x <- readSpatialData(pa))
 ```
 
-There are only `r length(SpatialData::shape(x, "cells"))` cells, but 
-`r format(length(SpatialData::point(x, "single_molecule")), big.mark=",")` 
+There are only `r length(spatialdataR::shape(x, "cells"))` cells, but 
+`r format(length(spatialdataR::point(x, "single_molecule")), big.mark=",")` 
 molecules, so that we downsample a random subset of 1,000 for visualization:
 
 ```{r merfish-plot, fig.width=6, fig.height=4}