--- a
+++ b/man/annotateSpatialData.Rd
@@ -0,0 +1,50 @@
+% 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")
+}
+}