--- a
+++ b/man/vrEmbeddingPlot.Rd
@@ -0,0 +1,59 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/visualization.R
+\name{vrEmbeddingPlot}
+\alias{vrEmbeddingPlot}
+\title{vrEmbeddingPlot}
+\usage{
+vrEmbeddingPlot(
+  object,
+  embedding = "pca",
+  group.by = "Sample",
+  group.ids = NULL,
+  split.by = NULL,
+  colors = NULL,
+  n.tile = 0,
+  assay = NULL,
+  ncol = 2,
+  nrow = NULL,
+  font.size = 5,
+  pt.size = 1,
+  label = FALSE,
+  common.legend = TRUE,
+  collapse.plots = TRUE
+)
+}
+\arguments{
+\item{object}{a VoltRon object}
+
+\item{embedding}{the embedding type, i.e. pca, umap etc.}
+
+\item{group.by}{a column of metadata from \link{Metadata} used as grouping label for the spatial entities}
+
+\item{group.ids}{a subset of categories defined in metadata column from \code{group.by}}
+
+\item{split.by}{a column of metadata from \link{Metadata} used as splitting spatial entities into ggplot panels, see \link{facet_wrap}}
+
+\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{ncol}{column wise number of plots, for \link{facet_wrap}}
+
+\item{nrow}{row wise number of plots, for \link{facet_wrap}}
+
+\item{font.size}{font size of labels, if label is TRUE}
+
+\item{pt.size}{point size}
+
+\item{label}{if TRUE, the labels of the ROI assays will be visualized}
+
+\item{common.legend}{whether to use a common legend for all plots, see \link{ggarrange}}
+
+\item{collapse.plots}{whether to combine all ggplots}
+}
+\description{
+Plotting embeddings of cells and spots on associated images from multiple assays in a VoltRon object.
+}