#' @include zzz.R

#'

NULL

####

# General ####

####

#' vrFeatures

#'

#' Get names of the features.

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#' 

#' @rdname vrFeatures

#' @export vrFeatures

#' @order 1

setGeneric("vrFeatures", function(object, ...) standardGeneric("vrFeatures"))

#' Feature Data

#'

#' Get and set feature data from the main.assay

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrFeatureData

#' @export vrFeatureData

#' @order 1

setGeneric("vrFeatureData", function(object, ...) standardGeneric("vrFeatureData"))

#' @rdname vrFeatureData

#' @export vrFeatureData<-

setGeneric("vrFeatureData<-", function(object, ..., value) standardGeneric("vrFeatureData<-"))

#' getFeatures

#'

#' Get variable features of assays

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname getFeatures

#' @export getFeatures

setGeneric("getFeatures", function(object, ...) standardGeneric("getFeatures"))

#' vrData

#'

#' Get data of assays

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrData

#' @export vrData

#' @order 1

setGeneric("vrData", function(object, ...) standardGeneric("vrData"))

#' generateTileData

#'

#' Generating data matrices for tile-based VoltRon objects from images

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname generateTileData

#' @export generateTileData

#' @order 1

setGeneric("generateTileData", function(object, ...) standardGeneric("generateTileData"))

#' changeSampleNames

#'

#' change sample names of VoltRon or other objects

#'

#' @param object a VoltRon or vrMetadata object.

#' @param ... arguments passed to other methods.

#'

#' @rdname changeSampleNames

#'

#' @noRd

setGeneric("changeSampleNames", function(object, ...) standardGeneric("changeSampleNames"))

#' changeAssayNames

#'

#' change assay names of VoltRon or other objects

#'

#' @param object a VoltRon, vrSample or vrLayer object.

#' @param ... arguments passed to other methods.

#'

#' @rdname changeAssayNames

#'

#' @noRd

setGeneric("changeAssayNames", function(object, ...) standardGeneric("changeAssayNames"))

####

# Assay ####

####

#' Main Assay

#'

#' Get and set the main assay of a VoltRon object

#' 

#' @param object a VoltRon object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrMainAssay

#' @export vrMainAssay

setGeneric("vrMainAssay", function(object, ...) standardGeneric("vrMainAssay"))

#' @param value new assay name

#' 

#' @rdname vrMainAssay

#' @export vrMainAssay<-

setGeneric("vrMainAssay<-", function(object, ..., value) standardGeneric("vrMainAssay<-"))

#' Update Assay

#'

#' update assays from vrAssay to vrAssayV2

#' 

#' @param object a VoltRon object.

#' @param ... arguments passed to other methods.

#'

#' @rdname updateAssay

#' @export updateAssay

setGeneric("updateAssay", function(object, ...) standardGeneric("updateAssay"))

#' Add Assay

#'

#' add a new assay (vrAssay object) to a VoltRon object

#'

#' @param object a VoltRon object.

#' @param ... arguments passed to other methods.

#'

#' @rdname addAssay

#' @export addAssay

setGeneric("addAssay", function(object, ...) standardGeneric("addAssay"))

#' Get Assay names

#'

#' Given a VoltRon, vrMetadata or vrAssay object, get/set names of assays.

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrAssayNames

#' @export vrAssayNames

#' @order 1

setGeneric("vrAssayNames", function(object, ...) standardGeneric("vrAssayNames"))

#' @rdname vrAssayNames

#' @noRd

setGeneric("vrAssayNames<-", function(object, ..., value) standardGeneric("vrAssayNames<-"))

#' Get assay types

#' 

#' Given a VoltRon or vrAssay object, get types of assays. 

#' Here, an assay type is of either tile, molecule, cell, spot or ROI.

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrAssayTypes

#' @export vrAssayTypes

#' @order 1

setGeneric("vrAssayTypes", function(object, ...) standardGeneric("vrAssayTypes"))

####

# Sample ####

####

#' Get Sample names

#'

#' Given a vrMetadata object, give names of samples

#'

#' @param object a vrMetadata object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrSampleNames

#' @export vrSampleNames

setGeneric("vrSampleNames", function(object, ...) standardGeneric("vrSampleNames"))

####

# Metadata ####

####

#' Metadata

#'

#' Get the metadata of a VoltRon object.

#'

#' @param object a VoltRon object.

#' @param ... arguments passed to other methods.

#'

#' @rdname Metadata

#' @export Metadata

setGeneric("Metadata", function(object, ...) standardGeneric("Metadata"))

#' @param value new metadata

#'

#' @rdname Metadata

setGeneric("Metadata<-", function(object, ..., value) standardGeneric("Metadata<-"))

####

# Processing ####

####

#' Normalize Data

#' 

#' Given a VoltRon or vrAssay object, normalize the raw count data.

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#' 

#' @rdname normalizeData

#' @export normalizeData

setGeneric("normalizeData", function(object, ...) standardGeneric("normalizeData"))

####

# Embedding ####

####

#' Get Embedding names

#'

#' Given a VoltRon or vrAssay object, give names of embeddings

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrEmbeddingNames

#' @export vrEmbeddingNames

#' @order 1

setGeneric("vrEmbeddingNames", function(object, ...) standardGeneric("vrEmbeddingNames"))

#' vrEmbeddings

#'

#' Given a VoltRon or vrAssay object, get embeddings of spatial points

#' 

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#' 

#' @rdname vrEmbeddings

#' @export vrEmbeddings

#' @order 1

setGeneric("vrEmbeddings", function(object, ...) standardGeneric("vrEmbeddings"))

#' @param value new embedding data

#'

#' @rdname vrEmbeddings

#' @export vrEmbeddings<-

setGeneric("vrEmbeddings<-", function(object, ..., value) standardGeneric("vrEmbeddings<-"))

####

# Feature ####

####

#' addFeature

#'

#' add a new feature set to a vrAssay (or VoltRon) object

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname addFeature

#' @export addFeature

#' @order 1

setGeneric("addFeature", function(object, ...) standardGeneric("addFeature"))

#' vrMainFeatureType

#'

#' Get the main feature type

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrMainFeatureType

#' @export vrMainFeatureType

#' @order 1

setGeneric("vrMainFeatureType", function(object, ...) standardGeneric("vrMainFeatureType"))

#' vrMainFeatureType

#'

#' Set the main image

#'

#' @param value the name of main feature set.

#'

#' @rdname vrMainFeatureType

#' @export vrMainFeatureType<-

setGeneric("vrMainFeatureType<-", function(object, ..., value) standardGeneric("vrMainFeatureType<-"))

#' vrFeatureTypeNames

#'

#' Get the names of the feature types

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrFeatureTypeNames

#' @export vrFeatureTypeNames

#' @order 1

setGeneric("vrFeatureTypeNames", function(object, ...) standardGeneric("vrFeatureTypeNames"))

####

# Spatial ####

####

#' vrSpatialPoints

#'

#' Get and set spatial entities.

#'

#' @param object a VoltRon, vrSample, vrLayer, vrAssay or vrSpatial object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrSpatialPoints

#' @export vrSpatialPoints

#' @order 1

#'

#' @examples

#' vrSpatialPoints(visium_data)

#' vrSpatialPoints(visium_data, assay = "Visium")

#' vrSpatialPoints(visium_data, assay = "Assay1")

setGeneric("vrSpatialPoints", function(object, ...) standardGeneric("vrSpatialPoints"))

#' @param value names for spatial points

#'

#' @rdname vrSpatialPoints

#' @export vrSpatialPoints<-

setGeneric("vrSpatialPoints<-", function(object, ..., value) standardGeneric("vrSpatialPoints<-"))

#' vrCoordinates

#'

#' Given a VoltRon, vrAssay or vrSpatial object, get and set the coordinates of assays and coordinate systems

#'

#' @param object a VoltRon, vrAssay or vrSpatial object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrCoordinates

#' @export vrCoordinates

#' @order 1

setGeneric("vrCoordinates", function(object, ...) standardGeneric("vrCoordinates"))

#' @param value coordinates

#' 

#' @rdname vrCoordinates

#' @export vrCoordinates<-

setGeneric("vrCoordinates<-", function(object, ..., value) standardGeneric("vrCoordinates<-"))

#' vrSegments

#'

#' Given a VoltRon, vrAssay or vrSpatial object, get and set the segment coordinates of assays and coordinate systems

#'

#' @param object a VoltRon, vrAssay or vrSpatial object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrSegments

#' @export vrSegments

#' @order 1

setGeneric("vrSegments", function(object, ...) standardGeneric("vrSegments"))

#' @param value segments

#' 

#' @rdname vrSegments

#' @export vrSegments<-

setGeneric("vrSegments<-", function(object, ..., value) standardGeneric("vrSegments<-"))

#' flipCoordinates

#'

#' Flip the coordinates of spatial points in the y axis direction. 

#'

#' @param object a VoltRon, vrAssay or vrSpatial object.

#' @param ... arguments passed to other methods.

#'

#' @rdname flipCoordinates

#' @export flipCoordinates

#' @order 1

setGeneric("flipCoordinates", function(object, ...) standardGeneric("flipCoordinates"))

####

# Image ####

####

#' vrImages

#'

#' Get images of VoltRon objects

#'

#' @param object a VoltRon, vrAssay or vrSpatial object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrImages

#' @export vrImages

#' @order 1

setGeneric("vrImages", function(object, ...) standardGeneric("vrImages"))

#' @param value a raster image or an image of \code{magick-image} object

#' 

#' @rdname vrImages

#' @export vrImages<-

setGeneric("vrImages<-", function(object, ..., value) standardGeneric("vrImages<-"))

#' vrImageNames

#'

#' Get names of all images

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrImageNames

#' @export vrImageNames

setGeneric("vrImageNames", function(object, ...) standardGeneric("vrImageNames"))

#' vrSpatialNames

#'

#' Get names of all spatial systems

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrSpatialNames

#' @export vrSpatialNames

setGeneric("vrSpatialNames", function(object, ...) standardGeneric("vrSpatialNames"))

#' vrImageChannelNames

#'

#' Get names of all image channels

#'

#' @param object a VoltRon, vrAssay or vrSpatial object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrImageChannelNames

#' @export vrImageChannelNames

#'

setGeneric("vrImageChannelNames", function(object, ...) standardGeneric("vrImageChannelNames"))

#' vrMainImage

#'

#' Get the main image

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrMainImage

#' @export vrMainImage

#' @order 1

setGeneric("vrMainImage", function(object, ...) standardGeneric("vrMainImage"))

#' vrMainSpatial

#'

#' Get the main spatial system name

#'

#' @param object a VoltRon or vrAssay object.

#' @param ... arguments passed to other methods.

#'

#' @rdname vrMainSpatial

#' @export vrMainSpatial

#' @order 1

setGeneric("vrMainSpatial", function(object, ...) standardGeneric("vrMainSpatial"))

#' vrMainImage

#'

#' Set the main image

#'

#' @param value the name of main spatial coordinate system.

#'

#' @rdname vrMainImage

#' @export vrMainImage<-

setGeneric("vrMainImage<-", function(object, ..., value) standardGeneric("vrMainImage<-"))

#' vrMainSpatial

#'

#' Set the main image

#'

#' @param value the name of main spatial coordinate system

#'

#' @rdname vrMainSpatial

#' @export vrMainSpatial<-

setGeneric("vrMainSpatial<-", function(object, ..., value) standardGeneric("vrMainSpatial<-"))

#' vrMainChannel

#'

#' Get and set the main channel name of the spatial system.

#' @param ... arguments passed to other methods.

#'

#' @param object a vrAssay or vrSpatial object

#'

#' @rdname vrMainChannel

#' @export vrMainChannel

#' @order 1

setGeneric("vrMainChannel", function(object, ...) standardGeneric("vrMainChannel"))

#' @param value the name of main channel of the spatial system

#'

#' @rdname vrMainChannel

#' @export vrMainChannel<-

setGeneric("vrMainChannel<-", function(object, ..., value) standardGeneric("vrMainChannel<-"))

#' resizeImage

#'

#' Resizing Magick images

#'

#' @param object a VoltRon, vrAssay or vrSpatial object.

#' @param ... arguments passed to other methods.

#'

#' @rdname resizeImage

#' @export resizeImage

#'

setGeneric("resizeImage", function(object, ...) standardGeneric("resizeImage"))

#' modulateImage

#'

#' Modulating Magick images

#'

#' @param object a VoltRon, vrAssay or vrSpatial object.

#' @param ... arguments passed to other methods.

#'

#' @rdname modulateImage

#' @export modulateImage

#'

setGeneric("modulateImage", function(object, ...) standardGeneric("modulateImage"))

#' combineChannels

#'

#' Combining channels into novel channels of the same image

#'

#' @param object a VoltRon, vrAssay or vrSpatial object.

#' @param ... arguments passed to other methods.

#'

#' @rdname combineChannels

#' @export combineChannels

#'

setGeneric("combineChannels", function(object, ...) standardGeneric("combineChannels"))

####

# Conversion ####

####

#' as.VoltRon

#'

#' Generic methods for conversion into a VoltRon object

#'

#' @param object a Seurat or SpatialExperiment object

#' @param ... Arguments passed to other methods

#'

#' @rdname as.VoltRon

#' @export as.VoltRon

as.VoltRon <- function(object, ...) {

  UseMethod(generic = 'as.VoltRon', object = object)

}

#' as.Zarr

#'

#' Generic methods to save VoltRon or magick-image objects as zarr files

#'

#' @param object a VoltRon or magick-image object

#' @param out_path output path to zarr file

#' @param image_id image name

#'

#' @rdname as.Zarr

#' @export as.Zarr

#'

as.Zarr <- function(object, out_path, image_id) {

  UseMethod(generic = 'as.Zarr', object = object)

}