--- a
+++ b/man/getEmbeddings.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/scAI_model.R
+\name{getEmbeddings}
+\alias{getEmbeddings}
+\title{compute the 2D coordinates of embeded cells, genes, loci and factors using VscAI visualization}
+\usage{
+getEmbeddings(object, genes.embed = NULL, loci.embed = NULL,
+  alpha.embed = 1.9, snn.embed = 5)
+}
+\arguments{
+\item{object}{scAI object}
+
+\item{genes.embed}{A vector of genes to be embedded}
+
+\item{loci.embed}{A vector of loci to be embedded}
+
+\item{alpha.embed}{Parameter controlling the distance between the cells and the factors}
+
+\item{snn.embed}{Number of neighbors}
+}
+\description{
+compute the 2D coordinates of embeded cells, genes, loci and factors using VscAI visualization
+}