% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/runTSCAN.R
\name{plotTSCANPseudotimeGenes}
\alias{plotTSCANPseudotimeGenes}
\title{Run plotTSCANPseudotimeGenes function to plot genes with significant 
changes}
\usage{
plotTSCANPseudotimeGenes(
  inSCE,
  pathIndex,
  direction = c("increasing", "decreasing"),
  n = 10
)
}
\arguments{
\item{inSCE}{Input \linkS4class{SingleCellExperiment} object.}

\item{pathIndex}{Path index for which the pseudotime values should be used. 
PathIndex corresponds to the terminal node of specific path from the root 
node to the terminal node.}

\item{direction}{Which direction to use. Choices are increasing or 
decreasing.}

\item{n}{An integer. Only to plot this number of top genes that are 
increasing/decreasing in expression with increasing pseudotime along 
the path in the MST. Default 10}
}
\value{
A plot with the top genes that increase/decrease in expression with 
increasing pseudotime along the path in the MST
}
\description{
A wrapper function which visualizes outputs from the 
\code{\link{runTSCANDEG}} function. Plots the genes that increase or decrease
in expression with increasing pseudotime along the path in the MST.
}
\examples{
data("scExample", package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
rowData(sce)$Symbol <- rowData(sce)$feature_name
rownames(sce) <- rowData(sce)$Symbol
sce <- runNormalization(sce, 
                        normalizationMethod = "LogNormalize", 
                        useAssay = "counts", 
                        outAssayName = "logcounts")
sce <- runDimReduce(inSCE = sce, 
                    method = "scaterPCA", 
                    useAssay = "logcounts", 
                    reducedDimName = "PCA")
sce <- runDimReduce(inSCE = sce, 
                    method = "rTSNE", 
                    useReducedDim = "PCA", 
                    reducedDimName = "TSNE")
sce <- runTSCAN (inSCE = sce, 
                 useReducedDim = "PCA", 
                 seed = NULL)
terminalNodes <- listTSCANTerminalNodes(sce, analysisName = "Pseudotime")
sce <- runTSCANDEG(inSCE = sce, 
                   pathIndex = terminalNodes[1])
plotTSCANPseudotimeGenes(inSCE = sce, 
                         pathIndex = terminalNodes[1], 
                         direction = "increasing")
}
\author{
Nida Pervaiz
}