--- a
+++ b/man/vrSpatialPlot.Rd
@@ -0,0 +1,109 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/visualization.R
+\name{vrSpatialPlot}
+\alias{vrSpatialPlot}
+\title{vrSpatialPlot}
+\usage{
+vrSpatialPlot(
+  object,
+  group.by = "Sample",
+  plot.segments = FALSE,
+  group.ids = NULL,
+  colors = NULL,
+  n.tile = 0,
+  assay = NULL,
+  graph.name = NULL,
+  graph.edge.color = "orange",
+  reduction = NULL,
+  ncol = 2,
+  nrow = NULL,
+  font.size = 2,
+  pt.size = 2,
+  cell.shape = 21,
+  alpha = 1,
+  label = FALSE,
+  spatial = NULL,
+  channel = NULL,
+  background.color = NULL,
+  background = NULL,
+  reg = FALSE,
+  crop = FALSE,
+  legend.pt.size = 2,
+  legend.text.size = 14,
+  scale.image = TRUE,
+  legend.loc = "right",
+  common.legend = TRUE,
+  collapse.plots = TRUE,
+  interactive = FALSE,
+  shiny.options = list()
+)
+}
+\arguments{
+\item{object}{a VoltRon object}
+
+\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{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{n.tile}{should points be aggregated into tiles before visualization (see \link{geom_tile}). Applicable only for cells and molecules}
+
+\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{graph.name}{if not NULL, the spatial graph is with name \code{graph.name} is visualized as well, see \link{vrGraphNames}}
+
+\item{graph.edge.color}{the colors of the graph edges, if \code{graph.name} is not NULL.}
+
+\item{reduction}{used by \code{vrSpatialPlotVitessce} to visualize an embedding alongside with the spatial plot.}
+
+\item{ncol}{column wise number of plots, for \link{ggarrange}}
+
+\item{nrow}{row wise number of plots, for \link{ggarrange}}
+
+\item{font.size}{font size}
+
+\item{pt.size}{point size}
+
+\item{cell.shape}{the shape of the points representing cells, see \link{geom_point}}
+
+\item{alpha}{alpha level of colors of visualized points and segments}
+
+\item{label}{if TRUE, the labels of the ROI assays will be visualized}
+
+\item{spatial}{the name of the main spatial system}
+
+\item{channel}{the name of the channel associated with the image}
+
+\item{background.color}{the color of plot background if a channel is not specified, or the spatial coord system doesnt have an image.}
+
+\item{background}{(DEPRECATED) the background of the plot. Either an image name, see \link{vrImageNames} or a vector of length two with image name 
+and a channel name, see \link{vrImageChannelNames}. Type "black" or "white" for black or white backgrounds. if NULL, the main image (\link{vrMainSpatial}) 
+and main channel (\link{vrMainChannel}) will be in the background. Otherwise the background will be grey.}
+
+\item{reg}{TRUE if registered coordinates of the main image (\link{vrMainSpatial}) is requested}
+
+\item{crop}{whether to crop an image of a spot assay to the extend of spots}
+
+\item{legend.pt.size}{the size of points at the legend}
+
+\item{legend.text.size}{the size of the text at the legend}
+
+\item{scale.image}{if TRUE, background image will be scaled down to a low resolution (width: 1000px)}
+
+\item{legend.loc}{the location of the legend, default is "right"}
+
+\item{common.legend}{whether to use a common legend for all plots, see \link{ggarrange}}
+
+\item{collapse.plots}{whether to combine all ggplots}
+
+\item{interactive}{if TRUE, run interactive plot}
+
+\item{shiny.options}{a list of shiny options (browser, host, port etc.) passed \code{options} arguement of \link{shinyApp}. For more information, see \link{runApp}}
+}
+\description{
+Plotting identification of spatially resolved cells, spots, and ROI on associated images from multiple assays in a VoltRon object.
+}