% 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}.

}