--- a
+++ b/man/addSpatialLayer.Rd
@@ -0,0 +1,59 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/visualization.R
+\name{addSpatialLayer}
+\alias{addSpatialLayer}
+\title{addSpatialLayer}
+\usage{
+addSpatialLayer(
+  g,
+  object,
+  assay,
+  group.by = "Sample",
+  plot.segments = FALSE,
+  group.ids = NULL,
+  reg = FALSE,
+  colors = NULL,
+  alpha = 1,
+  n.tile = 0,
+  pt.size = 2,
+  cell.shape = 21,
+  graph = NULL,
+  graph.edge.color = "orange",
+  spatial = NULL
+)
+}
+\arguments{
+\item{g}{ggplot object}
+
+\item{object}{a VoltRon object}
+
+\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{group.by}{a column of metadata from \link{Metadata} used as grouping label for the spatial entities}
+
+\item{plot.segments}{plot segments from \link{vrSegments} instead of points}
+
+\item{group.ids}{a subset of categories defined in metadata column from \code{group.by}}
+
+\item{reg}{TRUE if registered coordinates of the main image (\link{vrMainSpatial}) is requested}
+
+\item{colors}{the color set for group.by. Should be of the same size of group.id (if specified) or unique elements in group.by}
+
+\item{alpha}{alpha level of colors of visualized points and segments}
+
+\item{n.tile}{should points be aggregated into tiles before visualization (see \link{geom_tile}). Applicable only for cells and molecules}
+
+\item{pt.size}{point size}
+
+\item{cell.shape}{the shape of the points representing cells, see \link{geom_point}}
+
+\item{graph}{if not NULL, the graph is added to the plot}
+
+\item{graph.edge.color}{the color of graph edges, if \code{graph} is not NULL.}
+
+\item{spatial}{the name of the main spatial system}
+}
+\description{
+adding additional layers of spatial plots to an existing \link{vrSpatialPlot}.
+}