From 7c7ac878f69e3e39df22b2d7566bf2715db256f5 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 20 Jun 2024 12:48:49 -0400
Subject: [PATCH] Update exports

---
 NAMESPACE                     |  3 ---
 man/get_seurat_v5_obj.Rd      | 18 ++++++++++++++++++
 man/giotto_to_anndata_zarr.Rd | 25 -------------------------
 man/sce_to_anndata_zarr.Rd    |  2 +-
 man/seurat_to_anndata_zarr.Rd | 25 -------------------------
 man/spe_to_anndata_zarr.Rd    |  2 +-
 man/spe_to_ome_zarr.Rd        |  2 +-
 7 files changed, 21 insertions(+), 56 deletions(-)
 create mode 100644 man/get_seurat_v5_obj.Rd
 delete mode 100644 man/giotto_to_anndata_zarr.Rd
 delete mode 100644 man/seurat_to_anndata_zarr.Rd

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}