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update anndataR support, remove pizzarr #125

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update anndataR support, remove pizzarr #125

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11 changes: 4 additions & 7 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -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
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9 changes: 2 additions & 7 deletions R/read.R
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Expand Up @@ -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")
})
}

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