Yichen Wang authored on 31/03/2022 00:45:38
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\alias{plotClusterAbundance}
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\title{Plot the differential Abundance}
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\usage{
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-plotClusterAbundance(inSCE, cluster, variable) |
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+plotClusterAbundance(inSCE, cluster, variable, combinePlot = c("all", "none"))
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} |
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\arguments{
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\item{inSCE}{A \code{\link[SingleCellExperiment]{SingleCellExperiment}}
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@@ -15,9 +15,15 @@ cluster label in \code{\link{colData}}.}
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\item{variable}{A single \code{character}, specifying the name to store the
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phenotype labels in \code{\link{colData}}.}
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+ |
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+\item{combinePlot}{Must be either "all" or "none". "all" will combine all
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+plots into a single \code{\link[ggplot2]{ggplot}} object. Default
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+\code{"all"}.}
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} |
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\value{
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-A \code{list} with 4 \code{ggplot} objects.
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+When \code{combinePlot = "none"}, a \code{list} with 4
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+\code{\link[ggplot2]{ggplot}} objects; when \code{combinePlot = "all"}, a
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+single \code{\link[ggplot2]{ggplot}} object with for subplots.
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} |
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\description{
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Plot the differential Abundance |
Yichen Wang authored on 13/05/2021 21:09:54
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new file mode 100644 |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/abundance.R |
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+\name{plotClusterAbundance}
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+\alias{plotClusterAbundance}
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+\title{Plot the differential Abundance}
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+\usage{
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+plotClusterAbundance(inSCE, cluster, variable) |
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+} |
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+\arguments{
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+\item{inSCE}{A \code{\link[SingleCellExperiment]{SingleCellExperiment}}
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+object.} |
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+ |
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+\item{cluster}{A single \code{character}, specifying the name to store the
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+cluster label in \code{\link{colData}}.}
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+ |
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+\item{variable}{A single \code{character}, specifying the name to store the
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+phenotype labels in \code{\link{colData}}.}
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+} |
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+\value{
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+A \code{list} with 4 \code{ggplot} objects.
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+} |
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+\description{
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+Plot the differential Abundance |
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+} |
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+\details{
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+This function will visualize the differential abundance in two given |
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+variables, by making bar plots that presents the cell counting and fraction |
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+in different cases. |
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+} |
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+\examples{
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+data("mouseBrainSubsetSCE", package = "singleCellTK")
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+plotClusterAbundance(inSCE = mouseBrainSubsetSCE, |
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+ cluster = "tissue", |
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+ variable = "level1class") |
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+} |