--- a
+++ b/man/VscAIplot.Rd
@@ -0,0 +1,53 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/scAI_plotting.R
+\name{VscAIplot}
+\alias{VscAIplot}
+\title{VscAI visualize the genes, loci and factors that separate cell states on two dimensions alongside the cells}
+\usage{
+VscAIplot(object, gene.use, loci.use, loci.use.names, color.by,
+  labels.order = NULL, colors.use = NULL, brewer.use = FALSE,
+  xlabel = "VscAI1", ylabel = "VscAI2", title = NULL,
+  label.size = 3, cell.size = 0.3, font.size = 10, do.label = T,
+  show.legend = T, show.axes = T)
+}
+\arguments{
+\item{object}{scAI object}
+
+\item{gene.use}{embedded genes}
+
+\item{loci.use}{embedded loci}
+
+\item{loci.use.names}{alternative names of embedded loci, e.g, the corresponding motif}
+
+\item{color.by}{the name of the variable in pData, defining cell groups, cells are colored based on the labels}
+
+\item{labels.order}{defining the factor level}
+
+\item{colors.use}{defining the color for each cell group}
+
+\item{brewer.use}{use RColorBrewer palette instead of default ggplot2 color}
+
+\item{xlabel}{label of x-axis}
+
+\item{ylabel}{label of y-axis}
+
+\item{title}{main title of the plot}
+
+\item{label.size}{font size of the legend}
+
+\item{cell.size}{size of the dots}
+
+\item{font.size}{size of font}
+
+\item{do.label}{label the cluster in 2D space}
+
+\item{show.legend}{whether show the legend}
+
+\item{show.axes}{whether show the axes}
+}
+\value{
+ggplot2 object with 2D plot
+}
+\description{
+VscAI visualize the genes, loci and factors that separate cell states on two dimensions alongside the cells
+}