% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/allgenerics.R, R/objects.R, R/assay.R,

%   R/image.R

\name{vrCoordinates}

\alias{vrCoordinates}

\alias{vrCoordinates,VoltRon-method}

\alias{vrCoordinates,vrAssay-method}

\alias{vrCoordinates,vrAssayV2-method}

\alias{vrCoordinates,vrImage-method}

\alias{vrCoordinates,vrSpatial-method}

\alias{vrCoordinates<-,VoltRon-method}

\alias{vrCoordinates<-,vrAssay-method}

\alias{vrCoordinates<-,vrAssayV2-method}

\alias{vrCoordinates<-,vrImage-method}

\alias{vrCoordinates<-,vrSpatial-method}

\alias{vrCoordinates<-}

\title{vrCoordinates}

\usage{

vrCoordinates(object, ...)

\S4method{vrCoordinates}{VoltRon}(

  object,

  assay = NULL,

  image_name = NULL,

  spatial_name = NULL,

  reg = FALSE

)

\S4method{vrCoordinates}{vrAssay}(object, image_name = NULL, spatial_name = NULL, reg = FALSE)

\S4method{vrCoordinates}{vrAssayV2}(object, image_name = NULL, spatial_name = NULL, reg = FALSE)

\S4method{vrCoordinates}{vrImage}(object)

\S4method{vrCoordinates}{vrSpatial}(object)

\S4method{vrCoordinates}{VoltRon}(object, image_name = NULL, spatial_name = NULL, reg = FALSE) <- value

\S4method{vrCoordinates}{vrAssay}(object, image_name = NULL, spatial_name = NULL, reg = FALSE) <- value

\S4method{vrCoordinates}{vrAssayV2}(object, image_name = NULL, spatial_name = NULL, reg = FALSE) <- value

\S4method{vrCoordinates}{vrImage}(object) <- value

\S4method{vrCoordinates}{vrSpatial}(object) <- value

vrCoordinates(object, ...) <- value

}

\arguments{

\item{object}{a VoltRon, vrAssay or vrSpatial object.}

\item{...}{arguments passed to other methods.}

\item{assay}{assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. 

if NULL, the default assay will be used, see \link{vrMainAssay}.}

\item{image_name}{(deprecated, use \code{spatial_name}) the name/key of the image associated with the coordinates}

\item{spatial_name}{the name/key of the spatial system associated with the coordinates}

\item{reg}{TRUE if registered coordinates of the main image (\link{vrMainImage}) is requested}

\item{value}{coordinates}

}

\description{

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

}