diff --git a/NAMESPACE b/NAMESPACE index 2a43186..72cd43e 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -5,10 +5,8 @@ export(get_sce_obj) export(get_seurat_obj) export(get_seurat_v5_obj) export(get_spe_obj) -export(giotto_to_anndata_zarr) export(obj_list) export(sce_to_anndata_zarr) -export(seurat_to_anndata_zarr) export(spe_to_anndata_zarr) export(spe_to_ome_zarr) import(Seurat) @@ -22,7 +20,6 @@ importFrom(SummarizedExperiment,colData) importFrom(grDevices,as.raster) importFrom(grDevices,col2rgb) importFrom(methods,new) -importFrom(methods,slot) importFrom(stats,rnorm) importFrom(stats,rpois) importFrom(stats,runif) diff --git a/man/get_seurat_v5_obj.Rd b/man/get_seurat_v5_obj.Rd new file mode 100644 index 0000000..9b1e337 --- /dev/null +++ b/man/get_seurat_v5_obj.Rd @@ -0,0 +1,18 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mock_objects.R +\name{get_seurat_v5_obj} +\alias{get_seurat_v5_obj} +\title{Get a Seurat v5 object for tests and examples.} +\usage{ +get_seurat_v5_obj() +} +\value{ +The object. +} +\description{ +Get a Seurat v5 object for tests and examples. +} +\examples{ +obj <- get_seurat_v5_obj() +} +\keyword{internal} diff --git a/man/giotto_to_anndata_zarr.Rd b/man/giotto_to_anndata_zarr.Rd deleted file mode 100644 index 9f4a786..0000000 --- a/man/giotto_to_anndata_zarr.Rd +++ /dev/null @@ -1,25 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data_to_zarr.R -\name{giotto_to_anndata_zarr} -\alias{giotto_to_anndata_zarr} -\title{Save a Giotto object to an AnnData-Zarr store} -\usage{ -giotto_to_anndata_zarr(giotto_obj, out_path, X_slot = "raw_exprs") -} -\arguments{ -\item{giotto_obj}{The object to save.} - -\item{out_path}{A path to the output Zarr store.} - -\item{X_slot}{The name of the slot in the Giotto object to use for adata.X} -} -\value{ -TRUE if the conversion succeeds. -} -\description{ -Save a Giotto object to an AnnData-Zarr store -} -\examples{ -obj <- get_giotto_obj() -giotto_to_anndata_zarr(obj, "data/giotto.zarr") -} diff --git a/man/sce_to_anndata_zarr.Rd b/man/sce_to_anndata_zarr.Rd index 372681b..efe07b1 100644 --- a/man/sce_to_anndata_zarr.Rd +++ b/man/sce_to_anndata_zarr.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data_to_zarr.R +% Please edit documentation in R/bioc_to_zarr.R \name{sce_to_anndata_zarr} \alias{sce_to_anndata_zarr} \title{Save a SingleCellExperiment to an AnnData-Zarr store.} diff --git a/man/seurat_to_anndata_zarr.Rd b/man/seurat_to_anndata_zarr.Rd deleted file mode 100644 index 76633ff..0000000 --- a/man/seurat_to_anndata_zarr.Rd +++ /dev/null @@ -1,25 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data_to_zarr.R -\name{seurat_to_anndata_zarr} -\alias{seurat_to_anndata_zarr} -\title{Save a Seurat object to an AnnData-Zarr store.} -\usage{ -seurat_to_anndata_zarr(seurat_obj, out_path, assay) -} -\arguments{ -\item{seurat_obj}{The object to save.} - -\item{out_path}{A path to the output Zarr store.} - -\item{assay}{The name of the assay to save.} -} -\value{ -TRUE if the conversion succeeds. -} -\description{ -Save a Seurat object to an AnnData-Zarr store. -} -\examples{ -obj <- get_seurat_obj() -seurat_to_anndata_zarr(obj, out_path = "data/seurat.zarr", assay = "RNA") -} diff --git a/man/spe_to_anndata_zarr.Rd b/man/spe_to_anndata_zarr.Rd index 59596d8..0d340ef 100644 --- a/man/spe_to_anndata_zarr.Rd +++ b/man/spe_to_anndata_zarr.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data_to_zarr.R +% Please edit documentation in R/bioc_to_zarr.R \name{spe_to_anndata_zarr} \alias{spe_to_anndata_zarr} \title{Save a SpatialExperiment to an AnnData-Zarr store.} diff --git a/man/spe_to_ome_zarr.Rd b/man/spe_to_ome_zarr.Rd index bdbe5cb..d8cde20 100644 --- a/man/spe_to_ome_zarr.Rd +++ b/man/spe_to_ome_zarr.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data_to_zarr.R +% Please edit documentation in R/bioc_to_zarr.R \name{spe_to_ome_zarr} \alias{spe_to_ome_zarr} \title{Save an image in a SpatialExperiment to an OME-Zarr store}