@@ -43,5 +43,6 @@ sce <- runSeuratNormalizeData(sce, useAssay = "counts")

 sce <- runSeuratFindHVG(sce, useAssay = "counts")

 sce <- runSeuratScaleData(sce, useAssay = "counts")

 sce <- runSeuratPCA(sce, useAssay = "counts")

-plotSeuratReduction(sce, useReductionPlot = "pca")}

+plotSeuratReduction(sce, useReduction = "pca")

+}

 }

new file mode 100644

@@ -0,0 +1,47 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/seuratFunctions.R

+\name{plotSeuratReduction}

+\alias{plotSeuratReduction}

+\title{plotSeuratReduction

+Plots the selected dimensionality reduction method}

+\usage{

+plotSeuratReduction(

+  inSCE,

+  useReduction = c("pca", "ica", "tsne", "umap"),

+  showLegend = FALSE,

+  groupBy = NULL,

+  splitBy = NULL

+)

+}

+\arguments{

+\item{inSCE}{(sce) object which has the selected dimensionality reduction

+algorithm already computed and stored}

+

+\item{useReduction}{Dimentionality reduction to plot. One of "pca", "ica",

+"tsne", or "umap". Default \code{"umap"}.}

+

+\item{showLegend}{Select if legends and labels should be shown on the output

+plot or not. Either "TRUE" or "FALSE". Default \code{FALSE}.}

+

+\item{groupBy}{Specify a colData column name that be used for grouping.

+Default is \code{NULL}.}

+

+\item{splitBy}{Specify a colData column name that be used for splitting the

+output plot. Default is \code{NULL}.}

+}

+\value{

+plot object

+}

+\description{

+plotSeuratReduction

+Plots the selected dimensionality reduction method

+}

+\examples{

+data(scExample, package = "singleCellTK")

+\dontrun{

+sce <- runSeuratNormalizeData(sce, useAssay = "counts")

+sce <- runSeuratFindHVG(sce, useAssay = "counts")

+sce <- runSeuratScaleData(sce, useAssay = "counts")

+sce <- runSeuratPCA(sce, useAssay = "counts")

+plotSeuratReduction(sce, useReductionPlot = "pca")}

+}