deprecate read10xVisium in favor of VisiumIO functions

drighelli · Jun 21, 2024 · a996f8c · a996f8c
1 parent f742269
commit a996f8c
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Showing 26 changed files with 80 additions and 77 deletions.
diff --git a/R/SpatialExperiment-colData.R b/R/SpatialExperiment-colData.R
@@ -24,7 +24,7 @@
 #' @return a \code{\link{SpatialExperiment}} object with updated \code{colData}
 #' 
 #' @examples
-#' example(read10xVisium)
+#' example("SpatialExperiment-methods")
 #' 
 #' # empty replacement retains sample identifiers
 #' colData(spe) <- NULL

diff --git a/R/SpatialExperiment-combine.R b/R/SpatialExperiment-combine.R
@@ -45,7 +45,7 @@
 #' Dario Righelli
 #' 
 #' @examples
-#' example(read10xVisium, echo = FALSE)
+#' example(SpatialExperiment)
 #'
 #' # merging with duplicated 'sample_id's
 #' # will automatically assign unique identifiers

diff --git a/R/SpatialExperiment-methods.R b/R/SpatialExperiment-methods.R
@@ -89,7 +89,7 @@
 #' @return Return value varies depending on method, as described below.
 #' 
 #' @examples
-#' example(read10xVisium)
+#' example(SpatialExperiment)
 #' 
 #' # spatialCoords returns a numeric matrix
 #' head(spatialCoords(spe))

diff --git a/R/SpatialExperiment-rotate-mirror.R b/R/SpatialExperiment-rotate-mirror.R
@@ -65,7 +65,7 @@
 #' @author Nicholas J. Eagles
 #' 
 #' @examples
-#' example(read10xVisium)
+#' example(SpatialExperiment)
 #' 
 #' # rotateCoords(), mirrorCoords(), rotateObject(), and mirrorObject() return a
 #' # SpatialExperiment, potentially subsetted by sample.

diff --git a/R/SpatialExperiment.R b/R/SpatialExperiment.R
@@ -85,9 +85,9 @@
 #' To combine multiple samples within a single object, see
 #' \code{\link{combine}}.
 #' 
-#' For 10x Genomics Visium datasets, the function \code{\link{read10xVisium}}
-#' can be used to load data and create a \code{SpatialExperiment} object
-#' directly from Space Ranger output files.
+#' For 10x Genomics Visium datasets, the \code{\link[VisiumIO]{TENxVisiumList}} 
+#' and \code{\link[VisiumIO]{import}} functions can be used to load data into 
+#' a \code{SpatialExperiment} object directly from Space Ranger output files.
 #' 
 #' @seealso
 #' \code{?"\link{SpatialExperiment-methods}"}, which includes:
@@ -111,8 +111,6 @@
 #' 
 #' \code{\link{SpatialImage}}
 #' 
-#' \code{\link{read10xVisium}}
-#' 
 #' @author Dario Righelli and Helena L. Crowell
 #' 
 #' @return A \code{SpatialExperiment} object.
@@ -156,11 +154,19 @@
 #'     sample_id = "foo"))
 #'     
 #' #############################################################
-#' # Example 2: Spot-based ST (10x Visium) using 'read10xVisium'
+#' # Example 2: Spot-based ST (10x Visium) using 'VisiumIO'
 #' #############################################################
 #' 
-#' # see ?read10xVisium for details
-#' example(read10xVisium)
+#' library(VisiumIO)
+#' dir <- list.dirs(system.file(
+#'   file.path("extdata", "10xVisium"),
+#'   package = "SpatialExperiment"), 
+#'   recursive = FALSE, full.names = TRUE)
+#' (spe <- import(TENxVisiumList(
+#'   sampleFolders = dir, 
+#'   sample_ids = basename(dir), 
+#'   processing = "raw", 
+#'   images = "lowres")))
 #' 
 #' ##############################
 #' # Example 3: Molecule-based ST

diff --git a/R/imgData-methods.R b/R/imgData-methods.R
@@ -66,7 +66,7 @@
 #' with modified a \code{raster} matrix.
 #'   
 #' @examples
-#' example(read10xVisium)
+#' example(SpatialExperiment)
 #' 
 #' # 'SpatialImage' accession
 #' (spi <- getImg(spe))

diff --git a/R/read10xVisium.R b/R/read10xVisium.R
@@ -92,6 +92,8 @@ read10xVisium <- function(samples="",
     images="lowres",
     load=TRUE) {
 
+    .Deprecated("VisiumIO::TENxVisium(List)")
+
     # check if DropletUtils is installed
     if (!requireNamespace("DropletUtils", quietly = TRUE)) {
         warning("DropletUtils package must be installed to use read10xVisium()")

diff --git a/R/show.R b/R/show.R
@@ -14,7 +14,7 @@
 #' @author Dario Righelli and Helena L. Crowell
 #' 
 #' @examples
-#' example(read10xVisium)
+#' example(SpatialExperiment)
 #' spe
 NULL
 

diff --git a/R/subset.R b/R/subset.R
@@ -22,7 +22,7 @@
 #' @return a \code{\link{SpatialExperiment}} object
 #' 
 #' @examples
-#' example(read10xVisium)
+#' example(SpatialExperiment)
 #' 
 #' dim(spe)
 #' 

diff --git a/man/SpatialExperiment-colData.Rd b/man/SpatialExperiment-colData.Rd
diff --git a/man/SpatialExperiment-combine.Rd b/man/SpatialExperiment-combine.Rd
diff --git a/man/SpatialExperiment-methods.Rd b/man/SpatialExperiment-methods.Rd
diff --git a/man/SpatialExperiment-misc.Rd b/man/SpatialExperiment-misc.Rd
diff --git a/man/SpatialExperiment-rotate-mirror.Rd b/man/SpatialExperiment-rotate-mirror.Rd
diff --git a/man/SpatialExperiment-subset.Rd b/man/SpatialExperiment-subset.Rd
diff --git a/man/SpatialExperiment.Rd b/man/SpatialExperiment.Rd
diff --git a/man/imgData-methods.Rd b/man/imgData-methods.Rd
diff --git a/tests/testthat/test_SpatialExperiment-assays.R b/tests/testthat/test_SpatialExperiment-assays.R
@@ -1,4 +1,4 @@
-example(read10xVisium, echo = FALSE)
+example(SpatialExperiment, echo = FALSE)
 
 test_that("molecules()/<- gets/sets assay(., 'molecules')", {
     tmp <- spe

diff --git a/tests/testthat/test_SpatialExperiment-cbind.R b/tests/testthat/test_SpatialExperiment-cbind.R
@@ -1,4 +1,4 @@
-example(read10xVisium, echo = FALSE)
+example(SpatialExperiment, echo = FALSE)
 
 test_that("duplicated sample_ids are made unique with a message", {
     expect_message(new <- cbind(spe, spe))

diff --git a/tests/testthat/test_SpatialExperiment-colData.R b/tests/testthat/test_SpatialExperiment-colData.R
@@ -1,4 +1,4 @@
-example(read10xVisium, echo = FALSE)
+example(SpatialExperiment, echo = FALSE)
 
 test_that("colData()<-NULL retains only sample_id", {
     tmp <- spe

diff --git a/tests/testthat/test_SpatialExperiment-methods.R b/tests/testthat/test_SpatialExperiment-methods.R
@@ -1,4 +1,4 @@
-example(read10xVisium, echo = FALSE)
+example(SpatialExperiment, echo = FALSE)
 
 test_that("spatialData()", {
     spd <- spatialData(spe)

diff --git a/tests/testthat/test_SpatialExperiment-rotate-mirror.R b/tests/testthat/test_SpatialExperiment-rotate-mirror.R
@@ -1,4 +1,4 @@
-example(read10xVisium, echo = FALSE)
+example(SpatialExperiment, echo = FALSE)
 
 test_that("rotateCoords, non-null sample_id", {
     #   Subset followed by identity rotation should be equivalent to simply

diff --git a/tests/testthat/test_SpatialExperiment-subset.R b/tests/testthat/test_SpatialExperiment-subset.R
@@ -1,4 +1,4 @@
-example(read10xVisium, echo = FALSE)
+example(SpatialExperiment, echo = FALSE)
 
 test_that("missing i/j retains all", {
     expect_identical(spe, spe[, ])

diff --git a/tests/testthat/test_SpatialExperiment.R b/tests/testthat/test_SpatialExperiment.R
@@ -1,4 +1,4 @@
-example(read10xVisium, echo = FALSE)
+example(SpatialExperiment, echo = FALSE)
 
 test_that("empty constructor", {
     spe <- SpatialExperiment()

diff --git a/tests/testthat/test_imgData-methods.R b/tests/testthat/test_imgData-methods.R
@@ -1,4 +1,4 @@
-example(read10xVisium, echo = FALSE)
+example(SpatialExperiment, echo = FALSE)
 
 test_that("getImg/imgRaster/Source w/o imgData return NULL", {
     x <- spe