SpatialData -> spatialdataR (#29)

Co-authored-by: Hugo Gruson <git@hugogruson.fr>

Author: HelenaLC

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SpatialData.plot
 Title: SpatialData visualization
-Depends: R (>= 4.6), SpatialData
+Depends: R (>= 4.6), spatialdataR
 Version: 0.99.6
-Description: Visualization suit for 'SpatialData' (R). Current functionality 
+Description: Visualization suit for 'spatialdataR'. Current functionality 
     includes handling of multiscale 'images', visualizing 'labels', 'points', 
     and 'shapes'. For the latter, POINT, POLYGON, and MULTIPOLYGON geometries 
     are supported. For all but 'images', there is support to pass information 
@@ -49,7 +49,7 @@ Suggests:
     testthat,
     vdiffr
 Remotes:
-    HelenaLC/SpatialData,
+    HelenaLC/spatialdataR,
     HelenaLC/SpatialData.data
 biocViews: 
     Spatial,

NAMESPACE

@@ -5,16 +5,13 @@ exportMethods(plotImage)
 exportMethods(plotLabel)
 exportMethods(plotPoint)
 exportMethods(plotShape)
-import(SpatialData)
+import(spatialdataR)
 importFrom(DelayedArray,realize)
 importFrom(MatrixGenerics,rowQuantiles)
 importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,colData)
 importFrom(SingleCellExperiment,int_colData)
 importFrom(SingleCellExperiment,int_metadata)
-importFrom(SpatialData,channels)
-importFrom(SpatialData,data_type)
-importFrom(SpatialData,transform)
 importFrom(ggforce,geom_circle)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,annotation_raster)
@@ -49,4 +46,7 @@ importFrom(sf,st_as_sf)
 importFrom(sf,st_buffer)
 importFrom(sf,st_coordinates)
 importFrom(sf,st_geometry_type)
+importFrom(spatialdataR,channels)
+importFrom(spatialdataR,data_type)
+importFrom(spatialdataR,transform)
 importFrom(utils,tail)

R/data.R

@@ -8,6 +8,6 @@
 #'
 #' @examples
 #' x <- file.path("extdata", "blobs.zarr")
-#' x <- system.file(x, package="SpatialData")
+#' x <- system.file(x, package="spatialdataR")
 #' (x <- readSpatialData(x))
 NULL

R/plotFrame.R

@@ -10,7 +10,7 @@
 #'
 #' @examples
 #' x <- file.path("extdata", "blobs.zarr")
-#' x <- system.file(x, package="SpatialData")
+#' x <- system.file(x, package="spatialdataR")
 #' x <- readSpatialData(x)
 #'
 #' # shapes
@@ -36,7 +36,7 @@ NULL
 
 #' @importFrom sf st_as_sf st_coordinates st_geometry_type st_buffer
 #' @importFrom ggplot2 aes theme scale_type geom_sf coord_sf
-#' @importFrom SpatialData transform
+#' @importFrom spatialdataR transform
 #' @importFrom ggforce geom_circle
 #' @importFrom methods is
 #' @importFrom utils tail
@@ -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/plotImage.R

@@ -23,7 +23,7 @@
 #'
 #' @examples
 #' x <- file.path("extdata", "blobs.zarr")
-#' x <- system.file(x, package="SpatialData")
+#' x <- system.file(x, package="spatialdataR")
 #' x <- readSpatialData(x, tables=FALSE)
 #' 
 #' ms <- lapply(seq(3), \(.) 
@@ -39,7 +39,7 @@
 #' cl <- rep(list(c(0, 1/3)), 3)
 #' plotSpatialData() + plotImage(x, k=1, c=cmy, cl=cl)
 #' 
-#' @import SpatialData
+#' @import spatialdataR
 NULL
 
 .check_cl <- \(cl, d) {
@@ -139,7 +139,7 @@ NULL
 }
 
 # check if channels are indices or channel names
-#' @importFrom SpatialData channels
+#' @importFrom spatialdataR channels
 #' @noRd
 .ch_idx <- \(x, ch) {
     if (is.null(ch)) return(1)
@@ -158,15 +158,15 @@ NULL
 
 #' @importFrom methods as
 #' @importFrom DelayedArray realize
-#' @importFrom SpatialData data_type
+#' @importFrom spatialdataR data_type
 .df_i <- \(x, k=NULL, ch=NULL, c=NULL, cl=NULL) {
     a <- .get_multiscale_data(x, k)
     a <- a[.ch_idx(x, ch),,,drop=FALSE]
     a <- .norm_ia(a, data_type(x))
     a <- .prep_ia(a, c, cl)
 }
 
-#' @importFrom SpatialData transform
+#' @importFrom spatialdataR transform
 .get_wh <- \(x) {
     wh <- metadata(x)$wh
     if (!is.null(wh)) {

R/plotLabel.R

@@ -18,7 +18,7 @@
 #' @param nan character string; color for missing values (hidden by default).
 #' 
 #' @examples
-#' x <- system.file("extdata", "blobs.zarr", package="SpatialData")
+#' x <- system.file("extdata", "blobs.zarr", package="spatialdataR")
 #' x <- readSpatialData(x)
 #' 
 #' i <- "blobs_labels"
@@ -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]]