--- a
+++ b/man/cellVisualization.Rd
@@ -0,0 +1,48 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/scAI_plotting.R
+\name{cellVisualization}
+\alias{cellVisualization}
+\title{visualize cells in 2D-dimensional space}
+\usage{
+cellVisualization(object, cell_coords, color.by, labels.order = NULL,
+  colors.use = NULL, brewer.use = FALSE, xlabel = "UMAP1",
+  ylabel = "UMAP2", title = NULL, label.size = 4, cell.size = 0.3,
+  font.size = 10, do.label = F, show.legend = T, show.axes = T)
+}
+\arguments{
+\item{object}{scAI object}
+
+\item{cell_coords}{2D embedding coordinates of cells}
+
+\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 of cell groups}
+
+\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}{font size}
+
+\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{
+visualize cells in 2D-dimensional space
+}