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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plotTopHVG.R
\name{plotTopHVG}
\alias{plotTopHVG}
\title{Plot highly variable genes}
\usage{
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plotTopHVG(
inSCE,
method = c("vst", "mean.var.plot", "dispersion", "modelGeneVar"),
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hvgNumber = NULL,
useFeatureSubset = NULL,
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labelsCount = 20,
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featureDisplay = metadata(inSCE)$featureDisplay,
labelSize = 2,
dotSize = 2,
textSize = 12
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)
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}
\arguments{
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\item{inSCE}{Input \code{SingleCellExperiment} object containing the
computations.}
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\item{method}{Select either \code{"vst"}, \code{"mean.var.plot"},
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\code{"dispersion"} or \code{"modelGeneVar"}.}
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\item{hvgNumber}{Specify the number of top genes to highlight in red. Default
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\code{NULL}. See details.}
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\item{useFeatureSubset}{A character string for the \code{rowData} variable
name to store a logical index of selected features. Default \code{NULL}. See
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details.}
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\item{labelsCount}{Specify the number of data points/genes to label. Should
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be less than \code{hvgNumber}. Default \code{20}. See details.}
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\item{featureDisplay}{A character string for the \code{rowData} variable name
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to indicate what type of feature ID should be displayed. If set by
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\code{\link{setSCTKDisplayRow}}, will by default use it. If \code{NULL}, will
use \code{rownames(inSCE)}.}
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\item{labelSize}{Numeric, size of the text label on top HVGs. Default
\code{2}.}
\item{dotSize}{Numeric, size of the dots of the features. Default \code{2}.}
\item{textSize}{Numeric, size of the text of axis title, axis label, etc.
Default \code{12}.}
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}
\value{
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ggplot of HVG metrics and top HVG labels
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}
\description{
Plot highly variable genes
}
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\details{
When \code{hvgNumber = NULL} and \code{useFeature = NULL}, only plot
the mean VS variance/dispersion scatter plot. When only \code{hvgNumber} set,
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label the top \code{hvgNumber} HVGs ranked by the metrics calculated by
\code{method}. When \code{useFeatureSubset} set, label the features in
the subset on the scatter plot created with \code{method} and ignore
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\code{hvgNumber}.
}
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\examples{
data("mouseBrainSubsetSCE", package = "singleCellTK")
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mouseBrainSubsetSCE <- runModelGeneVar(mouseBrainSubsetSCE)
plotTopHVG(mouseBrainSubsetSCE, method = "modelGeneVar")
}
\seealso{
\code{\link{runFeatureSelection}}, \code{\link{runSeuratFindHVG}},
\code{\link{runModelGeneVar}}, \code{\link{getTopHVG}}
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}
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