% 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.

}