% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/annotation.R

\name{annotateSpatialData}

\alias{annotateSpatialData}

\title{annotateSpatialData}

\usage{

annotateSpatialData(

  object,

  label = "annotation",

  assay = NULL,

  annotation_assay = "ROIAnnotation",

  use.image.only = FALSE,

  shiny.options = list(launch.browser = getOption("shiny.launch.browser", interactive())),

  image_name = NULL,

  channel = NULL,

  ...

)

}

\arguments{

\item{object}{a VoltRon object}

\item{label}{the name of the new metadata column (default: annotation) annotating spatial points by selected polygons}

\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{annotation_assay}{name of the annotation assay ()}

\item{use.image.only}{if TRUE, use only the image}

\item{shiny.options}{a list of shiny options (launch.browser, host, port etc.) passed \code{options} arguement of \link{shinyApp}. For more information, see \link{runApp}}

\item{image_name}{the name/key of the image}

\item{channel}{the name of the main channel}

\item{...}{additional parameters passed to \link{vrSpatialPlot}.}

}

\description{

A mini shiny app to for annotating spatial points

}

\examples{

\dontrun{

# Annotate based on images

visium_data <- annotateSpatialData(visium_data, use.image.only = TRUE)

# Annotate based on spatial plot

xenium_data <- annotateSpatialData(xenium_data, group.by = "clusters")

}

}