% 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.

}