Merge pull request #86 from Artur-man/main

adding Covid-19 example to molecule analysis tutorial

NAMESPACE

@@ -6,30 +6,38 @@ S3method("Metadata<-",VoltRon)
 S3method("vrCoordinates<-",VoltRon)
 S3method("vrCoordinates<-",vrAssay)
 S3method("vrCoordinates<-",vrImage)
+S3method("vrCoordinates<-",vrSpatial)
 S3method("vrEmbeddings<-",VoltRon)
 S3method("vrEmbeddings<-",vrAssay)
 S3method("vrFeatureData<-",VoltRon)
 S3method("vrFeatureData<-",vrAssay)
 S3method("vrImages<-",vrAssay)
 S3method("vrImages<-",vrImage)
+S3method("vrImages<-",vrSpatial)
 S3method("vrMainChannel<-",vrAssay)
 S3method("vrMainChannel<-",vrImage)
+S3method("vrMainChannel<-",vrSpatial)
 S3method("vrMainImage<-",VoltRon)
 S3method("vrMainImage<-",vrAssay)
 S3method("vrSegments<-",VoltRon)
 S3method("vrSegments<-",vrAssay)
 S3method("vrSegments<-",vrImage)
+S3method("vrSegments<-",vrSpatial)
 S3method("vrSpatialPoints<-",vrAssay)
 S3method("vrSpatialPoints<-",vrImage)
+S3method("vrSpatialPoints<-",vrSpatial)
 S3method(Metadata,VoltRon)
 S3method(addAssay,VoltRon)
 S3method(addAssay,vrMetadata)
 S3method(as.VoltRon,Seurat)
 S3method(as.Zarr,"magick-image")
 S3method(as.Zarr,VoltRon)
+S3method(changeAssayNames,vrBlock)
+S3method(changeAssayNames,vrSample)
 S3method(combineChannels,VoltRon)
 S3method(combineChannels,vrAssay)
 S3method(combineChannels,vrImage)
+S3method(combineChannels,vrSpatial)
 S3method(flipCoordinates,VoltRon)
 S3method(flipCoordinates,vrAssay)
 S3method(getFeatures,VoltRon)
@@ -39,14 +47,17 @@ S3method(merge,vrMetadata)
 S3method(modulateImage,VoltRon)
 S3method(modulateImage,vrAssay)
 S3method(modulateImage,vrImage)
+S3method(modulateImage,vrSpatial)
 S3method(normalizeData,VoltRon)
 S3method(normalizeData,vrAssay)
 S3method(resizeImage,VoltRon)
 S3method(resizeImage,vrAssay)
 S3method(resizeImage,vrImage)
+S3method(resizeImage,vrSpatial)
 S3method(subset,VoltRon)
 S3method(subset,vrAssay)
 S3method(subset,vrImage)
+S3method(subset,vrSpatial)
 S3method(vrAssayNames,VoltRon)
 S3method(vrAssayNames,vrAssay)
 S3method(vrAssayNames,vrMetadata)
@@ -55,6 +66,7 @@ S3method(vrAssayTypes,vrAssay)
 S3method(vrCoordinates,VoltRon)
 S3method(vrCoordinates,vrAssay)
 S3method(vrCoordinates,vrImage)
+S3method(vrCoordinates,vrSpatial)
 S3method(vrData,VoltRon)
 S3method(vrData,vrAssay)
 S3method(vrEmbeddingNames,VoltRon)
@@ -68,25 +80,31 @@ S3method(vrFeatures,vrAssay)
 S3method(vrImageChannelNames,VoltRon)
 S3method(vrImageChannelNames,vrAssay)
 S3method(vrImageChannelNames,vrImage)
+S3method(vrImageChannelNames,vrSpatial)
 S3method(vrImageNames,VoltRon)
 S3method(vrImageNames,vrAssay)
 S3method(vrImages,VoltRon)
 S3method(vrImages,vrAssay)
 S3method(vrImages,vrImage)
+S3method(vrImages,vrSpatial)
 S3method(vrMainChannel,vrAssay)
 S3method(vrMainChannel,vrImage)
+S3method(vrMainChannel,vrSpatial)
 S3method(vrMainImage,VoltRon)
 S3method(vrMainImage,vrAssay)
 S3method(vrSampleNames,vrMetadata)
 S3method(vrSegments,VoltRon)
 S3method(vrSegments,vrAssay)
 S3method(vrSegments,vrImage)
+S3method(vrSegments,vrSpatial)
 S3method(vrSpatialPoints,VoltRon)
 S3method(vrSpatialPoints,vrAssay)
+S3method(vrSpatialPoints,vrBlock)
 S3method(vrSpatialPoints,vrImage)
 S3method(vrSpatialPoints,vrLayer)
 S3method(vrSpatialPoints,vrMetadata)
 S3method(vrSpatialPoints,vrSample)
+S3method(vrSpatialPoints,vrSpatial)
 export("Metadata<-")
 export("vrAssayNames<-")
 export("vrCoordinates<-")
@@ -178,6 +196,7 @@ exportClasses(vrImage)
 exportClasses(vrLayer)
 exportClasses(vrMetadata)
 exportClasses(vrSample)
+exportClasses(vrSpatial)
 exportMethods("[[")
 exportMethods("[[<-")
 import(ggplot2)

R/generics.R

@@ -514,6 +514,6 @@ as.VoltRon <- function(object, ...) {
 #' @rdname as.Zarr
 #' @export as.Zarr
 #'
-as.Zarr <- function(object, ...) {
+as.Zarr <- function(object, out_path, image_id) {
   UseMethod(generic = 'as.Zarr', object = object)
 }