% 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.

}