--- a
+++ b/man/vrSpatialFeaturePlot.Rd
@@ -0,0 +1,103 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/visualization.R
+\name{vrSpatialFeaturePlot}
+\alias{vrSpatialFeaturePlot}
+\title{vrSpatialFeaturePlot}
+\usage{
+vrSpatialFeaturePlot(
+  object,
+  features,
+  combine.features = FALSE,
+  group.by = "label",
+  plot.segments = FALSE,
+  n.tile = 0,
+  norm = TRUE,
+  log = FALSE,
+  assay = NULL,
+  graph.name = NULL,
+  ncol = 2,
+  nrow = NULL,
+  font.size = 2,
+  pt.size = 2,
+  cell.shape = 16,
+  title.size = 10,
+  alpha = 0.6,
+  keep.scale = "feature",
+  label = FALSE,
+  spatial = NULL,
+  channel = NULL,
+  background.color = NULL,
+  background = NULL,
+  reg = FALSE,
+  crop = FALSE,
+  scale.image = TRUE,
+  common.legend = FALSE,
+  legend.loc = "right",
+  collapse.plots = TRUE
+)
+}
+\arguments{
+\item{object}{a VoltRon object}
+
+\item{features}{a set of features to be visualized, either from \link{vrFeatures} of raw or normalized data or columns of the \link{Metadata}.}
+
+\item{combine.features}{whether to combine all features in one plot}
+
+\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{n.tile}{should points be aggregated into tiles before visualization (see \link{geom_tile}). Applicable only for cells and molecules}
+
+\item{norm}{if TRUE, the normalized data is used}
+
+\item{log}{if TRUE, data features (excluding metadata features) will be log transformed}
+
+\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{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{title.size}{title size of legend and plot}
+
+\item{alpha}{alpha level of colors of visualized points and segments}
+
+\item{keep.scale}{whether unify all scales for all features or not}
+
+\item{label}{if TRUE, labels of ROIs will be visualized too}
+
+\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{scale.image}{if TRUE, background image will be scaled down to a low resolution (width: 1000px)}
+
+\item{common.legend}{whether to use a common legend for all plots, see \link{ggarrange}}
+
+\item{legend.loc}{the location of the legend, default is "right"}
+
+\item{collapse.plots}{whether to combine all ggplots}
+}
+\description{
+Plotting single/multiple features of spatially resolved cells, spots, and ROI on associated images from multiple assays in a VoltRon object.
+}