Merge pull request #140 from lmweber/DropletUtils_dependencies

Move DropletUtils to Suggests to reduce dependencies

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: SpatialExperiment
-Version: 1.11.1
+Version: 1.11.2
 Title: S4 Class for Spatially Resolved -omics Data
 Description: Defines an S4 class for storing data from spatial -omics experiments. 
     The class extends SingleCellExperiment to 
@@ -41,14 +41,14 @@ Imports:
     utils, 
     S4Vectors, 
     SummarizedExperiment, 
-    DropletUtils, 
     BiocGenerics, 
     BiocFileCache
 Suggests: 
     knitr, 
     rmarkdown, 
     testthat, 
     BiocStyle, 
-    BumpyMatrix
+    BumpyMatrix, 
+    DropletUtils
 VignetteBuilder: knitr
 RoxygenNote: 7.2.3

NAMESPACE

@@ -71,7 +71,6 @@ exportMethods(spatialDataNames)
 importClassesFrom(S4Vectors,Annotated)
 importFrom(BiocGenerics,cbind)
 importFrom(BiocGenerics,rbind)
-importFrom(DropletUtils,read10xCounts)
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,coolcat)
 importFrom(S4Vectors,isEmpty)

R/read10xVisium.R

@@ -14,7 +14,7 @@
 #'   ignored if \code{!is.null(names(samples))}
 #' @param type character string specifying 
 #'   the type of format to read count data from
-#'   (see \code{\link{read10xCounts}})
+#'   (see \code{read10xCounts})
 #' @param data character string specifying whether to read in
 #'   filtered (spots mapped to tissue) or raw data (all spots).
 #' @param images character vector specifying which images to include. 
@@ -81,7 +81,6 @@
 #' imgData(spe)
 #' 
 #' @importFrom rjson fromJSON
-#' @importFrom DropletUtils read10xCounts
 #' @importFrom methods as
 #' @importFrom S4Vectors DataFrame 
 #' @importFrom SummarizedExperiment assays rowData
@@ -93,6 +92,11 @@ read10xVisium <- function(samples="",
     images="lowres",
     load=TRUE) {
 
+    # check if DropletUtils is installed
+    if (!requireNamespace("DropletUtils", quietly = TRUE)) {
+        warning("DropletUtils package must be installed to use read10xVisium()")
+    }
+
     # check validity of input arguments
     type <- match.arg(type)
     data <- match.arg(data)
@@ -160,7 +164,7 @@ read10xVisium <- function(samples="",
     # read spatial coordinates
     spel <- lapply(seq_along(counts), function(i) {
         # read count data as 'SingleCellExperiment'
-        sce <- read10xCounts(
+        sce <- DropletUtils::read10xCounts(
             samples=counts[i], 
             sample.names=sids[i],
             col.names=TRUE)

inst/NEWS

@@ -1,3 +1,6 @@
+changes in version 1.11.2 (2023-09-01)
++ move DropletUtils package to Suggests
+
 changes in version 1.11.1 (2023-08-21)
 + add methods to rotate/mirror spatial coordinates and objects