% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/abundance.R
 \name{plotClusterAbundance}
 \alias{plotClusterAbundance}
 \title{Plot the differential Abundance}
 \usage{

 plotClusterAbundance(inSCE, cluster, variable, combinePlot = c("all", "none"))

 }
 \arguments{
 \item{inSCE}{A \code{\link[SingleCellExperiment]{SingleCellExperiment}}
 object.}
 
 \item{cluster}{A single \code{character}, specifying the name to store the
 cluster label in \code{\link{colData}}.}
 
 \item{variable}{A single \code{character}, specifying the name to store the
 phenotype labels in \code{\link{colData}}.}

 
 \item{combinePlot}{Must be either "all" or "none". "all" will combine all 
 plots into a single \code{\link[ggplot2]{ggplot}} object. Default 
 \code{"all"}.}

 }
 \value{

 When \code{combinePlot = "none"}, a \code{list} with 4 
 \code{\link[ggplot2]{ggplot}} objects; when \code{combinePlot = "all"}, a 
 single \code{\link[ggplot2]{ggplot}} object with for subplots.

 }
 \description{
 Plot the differential Abundance
 }
 \details{
 This function will visualize the differential abundance in two given
 variables, by making bar plots that presents the cell counting and fraction
 in different cases.
 }
 \examples{
 data("mouseBrainSubsetSCE", package = "singleCellTK")
 plotClusterAbundance(inSCE = mouseBrainSubsetSCE,
                      cluster = "tissue",
                      variable = "level1class")
 }