update docs & NAMESPACE

Author: HelenaLC

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SpatialData
 Title: Representation of Python's SpatialData in R
-Depends: R (>= 4.4)
+Depends: R (>= 4.4), S7
 Version: 0.99.23
 Description: Interface to Python's 'SpatialData', currently including:
     reticulate-based use of 'spatialdata-io' for reading of manufracturer
@@ -82,7 +82,7 @@ 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

NAMESPACE

@@ -1,152 +1,55 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(.DollarNames,PointFrame)
-S3method(.DollarNames,ShapeFrame)
-S3method(.DollarNames,SpatialData)
-S3method(.DollarNames,Zattrs)
-S3method(filter,PointFrame)
-S3method(select,PointFrame)
-export(.SpatialData)
 export(ImageArray)
 export(LabelArray)
 export(PointFrame)
 export(ShapeFrame)
 export(SpatialData)
-export(Zattrs)
-export(do_tx_to_ext)
-export(mask)
-export(plotCoordGraph)
 export(readImage)
 export(readLabel)
 export(readPoint)
 export(readShape)
 export(readSpatialData)
 export(readTable)
-exportClasses(SpatialData)
-exportMethods("$")
-exportMethods("[")
-exportMethods("[[")
-exportMethods("[[<-")
-exportMethods("image<-")
-exportMethods("images<-")
-exportMethods("label<-")
-exportMethods("labels<-")
-exportMethods("point<-")
-exportMethods("points<-")
-exportMethods("shape<-")
-exportMethods("shapes<-")
-exportMethods("table<-")
-exportMethods("tables<-")
-exportMethods(CTdata)
-exportMethods(CTgraph)
-exportMethods(CTname)
-exportMethods(CTpath)
-exportMethods(CTtype)
-exportMethods(addCT)
-exportMethods(as.data.frame)
-exportMethods(axes)
-exportMethods(channels)
-exportMethods(colnames)
-exportMethods(data)
-exportMethods(dim)
-exportMethods(element)
-exportMethods(getTable)
-exportMethods(hasTable)
-exportMethods(image)
-exportMethods(imageNames)
-exportMethods(images)
-exportMethods(label)
-exportMethods(labelNames)
-exportMethods(labels)
-exportMethods(layer)
-exportMethods(length)
-exportMethods(mask)
-exportMethods(meta)
-exportMethods(names)
-exportMethods(point)
-exportMethods(pointNames)
-exportMethods(points)
-exportMethods(query)
-exportMethods(rmvCT)
-exportMethods(rotate)
-exportMethods(rownames)
-exportMethods(scale)
-exportMethods(setTable)
-exportMethods(shape)
-exportMethods(shapeNames)
-exportMethods(shapes)
-exportMethods(table)
-exportMethods(tableNames)
-exportMethods(tables)
-exportMethods(translation)
-exportMethods(valTable)
+export(sd_make)
+export(sd_osn_list)
+export(sd_osn_load)
+export(sd_plot)
+export(sd_plot_image)
+export(sdio_list)
 import(geoarrow)
-importClassesFrom(S4Arrays,Array)
-importClassesFrom(S4Vectors,DFrame)
-importFrom(BiocGenerics,as.data.frame)
-importFrom(BiocGenerics,colnames)
-importFrom(BiocGenerics,rownames)
+import(ggplot2)
 importFrom(DelayedArray,realize)
-importFrom(Matrix,rowSums)
-importFrom(Matrix,sparseVector)
-importFrom(Matrix,t)
-importFrom(RBGL,sp.between)
 importFrom(Rarr,ZarrArray)
-importFrom(S4Arrays,as.array.Array)
+importFrom(Rarr,read_zarr_attributes)
+importFrom(Rarr,zarr_overview)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,coolcat)
 importFrom(S4Vectors,isSequence)
-importFrom(S4Vectors,make_zero_col_DFrame)
 importFrom(S4Vectors,metadata)
-importFrom(S4Vectors,setValidity2)
+importFrom(S7,"method<-")
+importFrom(S7,S4_register)
+importFrom(S7,S7_class)
+importFrom(S7,S7_inherits)
+importFrom(S7,check_is_S7)
+importFrom(S7,class_any)
+importFrom(S7,class_data.frame)
+importFrom(S7,class_list)
+importFrom(S7,method)
+importFrom(S7,new_S3_class)
+importFrom(S7,new_class)
+importFrom(S7,new_generic)
+importFrom(S7,new_union)
 importFrom(SingleCellExperiment,"int_colData<-")
 importFrom(SingleCellExperiment,"int_metadata<-")
-importFrom(SingleCellExperiment,SingleCellExperiment)
 importFrom(SingleCellExperiment,int_colData)
 importFrom(SingleCellExperiment,int_metadata)
 importFrom(SummarizedExperiment,"colData<-")
-importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,colData)
+importFrom(anndataR,read_zarr)
 importFrom(arrow,open_dataset)
-importFrom(basilisk,BasiliskEnvironment)
-importFrom(basilisk,basiliskRun)
-importFrom(basilisk,basiliskStart)
-importFrom(basilisk,basiliskStop)
-importFrom(dplyr,all_of)
-importFrom(dplyr,collect)
-importFrom(dplyr,filter)
-importFrom(dplyr,mutate)
-importFrom(dplyr,pull)
-importFrom(dplyr,select)
-importFrom(graph,"edgeData<-")
-importFrom(graph,"edgeDataDefaults<-")
-importFrom(graph,"nodeData<-")
-importFrom(graph,"nodeDataDefaults<-")
-importFrom(graph,"nodes<-")
-importFrom(graph,addEdge)
-importFrom(graph,addNode)
-importFrom(graph,edgeData)
-importFrom(graph,graph.par)
-importFrom(graph,graphAM)
-importFrom(graph,nodeData)
-importFrom(graph,nodes)
-importFrom(jsonlite,fromJSON)
+importFrom(grDevices,col2rgb)
+importFrom(grDevices,rgb)
 importFrom(methods,as)
-importFrom(methods,callNextMethod)
 importFrom(methods,is)
-importFrom(methods,new)
-importFrom(methods,setClassUnion)
-importFrom(methods,setReplaceMethod)
-importFrom(reticulate,import)
-importFrom(sf,"st_geometry<-")
-importFrom(sf,st_as_sf)
-importFrom(sf,st_coordinates)
-importFrom(sf,st_distance)
-importFrom(sf,st_geometry)
-importFrom(sf,st_geometry_type)
-importFrom(sf,st_point)
-importFrom(sf,st_sfc)
 importFrom(utils,.DollarNames)
-importFrom(utils,head)
-importFrom(utils,tail)
-importFrom(zellkonverter,AnnData2SCE)

R/data.R

@@ -19,9 +19,6 @@
 #'
 #' # retrieve dataset & ingest
 #' (sd <- sd_osn_load("merfish"))
-#' 
-#' @importFrom SpatialData readSpatialData
-#' @importClassesFrom SpatialData SpatialData
 NULL
 
 #' @rdname sd_data