--- a
+++ b/man/vrEmbeddingFeaturePlot.Rd
@@ -0,0 +1,59 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/visualization.R
+\name{vrEmbeddingFeaturePlot}
+\alias{vrEmbeddingFeaturePlot}
+\title{vrEmbeddingFeaturePlot}
+\usage{
+vrEmbeddingFeaturePlot(
+  object,
+  embedding = "pca",
+  features = NULL,
+  combine.features = FALSE,
+  n.tile = 0,
+  norm = TRUE,
+  log = FALSE,
+  assay = NULL,
+  ncol = 2,
+  nrow = NULL,
+  font.size = 2,
+  pt.size = 1,
+  keep.scale = "feature",
+  common.legend = TRUE,
+  collapse.plots = TRUE
+)
+}
+\arguments{
+\item{object}{a VoltRon object}
+
+\item{embedding}{the embedding type, i.e. pca, umap etc.}
+
+\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{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{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{keep.scale}{whether unify all scales for all features or not}
+
+\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 features of spatially resolved cells and spots on embeddings from multiple assays in a VoltRon object.
+}