diff --git a/DESCRIPTION b/DESCRIPTION index 9e2249b..615fdc6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -63,13 +63,10 @@ Suggests: SpatialData.data, SpatialData.plot, testthat, - DT -Enhances: - anndataR, - pizzarr + DT, + anndataR Remotes: - keller-mark/pizzarr, - keller-mark/anndataR@spatialdata, + keller-mark/anndataR@keller-mark/zarr, HelenaLC/SpatialData.data, HelenaLC/SpatialData.plot biocViews: @@ -82,7 +79,7 @@ biocViews: SingleCell, Spatial License: Artistic-2.0 -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 Encoding: UTF-8 VignetteBuilder: knitr URL: https://github.com/HelenaLC/SpatialData diff --git a/R/read.R b/R/read.R index 929fd14..3c951a8 100644 --- a/R/read.R +++ b/R/read.R @@ -150,15 +150,10 @@ readShape <- function(x, ...) { .readTable_anndataR <- function(x) { if (!requireNamespace('anndataR', quietly=TRUE)) { stop("To use this function, install the 'anndataR' package via\n", - "`BiocManager::install(\"keller-mark/anndataR\", ref=\"spatialdata\")`") - } - if (!requireNamespace('pizzarr', quietly=TRUE)) { - stop("To use this function, install the 'pizzarr' package via\n", - "`BiocManager::install(\"keller-mark/pizzarr\")`") + "`BiocManager::install(\"keller-mark/anndataR\", ref=\"keller-mark/zarr\")`") } suppressWarnings({ # suppress warnings related to hidden files - adata <- anndataR::read_zarr(x) - anndataR::to_SingleCellExperiment(adata) + adata <- anndataR::read_zarr(x, as = "SingleCellExperiment") }) }