@@ -2,65 +2,62 @@

 % Please edit documentation in R/runTSCAN.R

 \name{plotTSCANPseudotimeGenes}

 \alias{plotTSCANPseudotimeGenes}

-\title{Run plotTSCANPseudotimeGenes function to plot genes with significant 

-changes}

+\title{Plot expression changes of top features along a TSCAN pseudotime path}

 \usage{

 plotTSCANPseudotimeGenes(

   inSCE,

   pathIndex,

   direction = c("increasing", "decreasing"),

-  n = 10

+  topN = 10,

+  useAssay = NULL,

+  featureDisplay = metadata(inSCE)$featureDisplay

 )

 }

 \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{pathIndex}{Path index for which the pseudotime values should be used.

+Should have being used in \code{\link{runTSCANDEG}}.}

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

-decreasing.}

+\item{direction}{Should we show features with expression increasing or

+decreeasing along the increase in TSCAN pseudotime? Choices are

+\code{"increasing"} or \code{"decreasing"}.}

-\item{n}{An integer. Only to plot this number of top genes that are 

-increasing/decreasing in expression with increasing pseudotime along 

+\item{topN}{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}

+

+\item{useAssay}{A single character to specify a feature expression matrix in

+\code{assays} slot. The expression of top features from here will be

+visualized. Default \code{NULL} use the one used for

+\code{\link{runTSCANDEG}}.}

+

+\item{featureDisplay}{Specify the feature ID type to display. Users can set

+default value with \code{\link{setSCTKDisplayRow}}. \code{NULL} or

+\code{"rownames"} specifies the rownames of \code{inSCE}. Other character

+values indicates \code{rowData} variable.}

 }

 \value{

-A plot with the top genes that increase/decrease in expression with 

-increasing pseudotime along the path in the MST

+A \code{.ggplot} object with the facets of the top genes. Expression

+on y-axis, pseudotime on x-axis.

 }

 \description{

-A wrapper function which visualizes outputs from the 

+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.

+\code{\link{runTSCANDEG}} has to be run in advance with using the same

+\code{pathIndex} of interest.

 }

 \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")

+data("mouseBrainSubsetSCE", package = "singleCellTK")

+mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,

+                                useReducedDim = "PCA_logcounts")

+terminalNodes <- listTSCANTerminalNodes(mouseBrainSubsetSCE)

+mouseBrainSubsetSCE <- runTSCANDEG(inSCE = mouseBrainSubsetSCE,

+                                   pathIndex = terminalNodes[1])

+plotTSCANPseudotimeGenes(mouseBrainSubsetSCE,

+                         pathIndex = terminalNodes[1],

+                         useAssay = "logcounts")

 }

 \author{

 Nida Pervaiz

@@ -15,13 +15,16 @@ plotTSCANPseudotimeGenes(

 \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{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{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}

+\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 

@@ -37,12 +40,26 @@ 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)

-sce <- runTSCANDEG(inSCE = sce, pathIndex = 4)

-plotTSCANPseudotimeGenes(inSCE = sce, pathIndex = 4, 

+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{

@@ -15,16 +15,13 @@ plotTSCANPseudotimeGenes(

 \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{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 \code{10}.}

+\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 

@@ -14,8 +14,8 @@ plotTSCANPseudotimeGenes(

 \arguments{

 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object.}

-\item{pathIndex}{Path number for which the pseudotime values should be used. PathIndex 

-corresponds to one path from the root node to one of the terminal nodes.}

+\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.}

@@ -36,7 +36,7 @@ data("scExample", package = "singleCellTK")

 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")

 rowData(sce)$Symbol <- rowData(sce)$feature_name

 rownames(sce) <- rowData(sce)$Symbol

-sce <- scaterlogNormCounts(sce, assayName = "logcounts")

+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)

@@ -2,7 +2,8 @@

 % Please edit documentation in R/runTSCAN.R

 \name{plotTSCANPseudotimeGenes}

 \alias{plotTSCANPseudotimeGenes}

-\title{Run plotTSCANPseudotimeGenes function to plot genes with significant changes}

+\title{Run plotTSCANPseudotimeGenes function to plot genes with significant 

+changes}

 \usage{

 plotTSCANPseudotimeGenes(

   inSCE,

@@ -14,22 +15,25 @@ plotTSCANPseudotimeGenes(

 \arguments{

 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object.}

-\item{pathIndex}{Path number for which the pseudotime values should be used. PathIndex 

-corresponds to one path from the root node to one of the terminal nodes.}

+\item{pathIndex}{Path number for which the pseudotime values should be used. 

+PathIndex corresponds to one path from the root node to one of the terminal 

+nodes.}

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

+\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}

+\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 \code{10}.}

 }

 \value{

-A plot with the top genes that increase/decrease in expression with increasing 

-pseudotime along the path in the MST

+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 runTSCANDEG function. 

-Plots the genes that increase or decrease in expression with increasing pseudotime along 

-the path in the MST

+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")

@@ -37,11 +41,14 @@ sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")

 rowData(sce)$Symbol <- rowData(sce)$feature_name

 rownames(sce) <- rowData(sce)$Symbol

 sce <- scaterlogNormCounts(sce, assayName = "logcounts")

-sce <- runDimReduce(inSCE = sce, method = "scaterPCA", useAssay = "logcounts", reducedDimName = "PCA")

-sce <- runDimReduce(inSCE = sce, method = "rTSNE", useReducedDim = "PCA", reducedDimName = "TSNE")

+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)

 sce <- runTSCANDEG(inSCE = sce, pathIndex = 4)

-plotTSCANPseudotimeGenes(inSCE = sce, pathIndex = 4, direction = "increasing")

+plotTSCANPseudotimeGenes(inSCE = sce, pathIndex = 4, 

+                         direction = "increasing")

 }

 \author{

 Nida Pervaiz

@@ -34,14 +34,14 @@ 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 <- singleCellTK::scaterlogNormCounts(sce, assayName = "logcounts")

-sce <- scater::runPCA(sce)

-sce <- scater::runTSNE (sce, dimred = "PCA")

+rowData(sce)$Symbol <- rowData(sce)$feature_name

+rownames(sce) <- rowData(sce)$Symbol

+sce <- scaterlogNormCounts(sce, assayName = "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)

-sce <- runTSCANDEG(inSCE = sce, pathIndex = 3)

-plotTSCANPseudotimeGenes(inSCE = sce, pathIndex = 3, direction = "increasing")

+sce <- runTSCANDEG(inSCE = sce, pathIndex = 4)

+plotTSCANPseudotimeGenes(inSCE = sce, pathIndex = 4, direction = "increasing")

 }

 \author{

 Nida Pervaiz

@@ -14,17 +14,22 @@ plotTSCANPseudotimeGenes(

 \arguments{

 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object.}

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

+\item{pathIndex}{Path number for which the pseudotime values should be used. PathIndex 

+corresponds to one path from the root node to one of the terminal nodes.}

 \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}

+\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

+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 runTSCANDEG function. Plots the genes that increase or decrease in expression with increasing pseudotime along the path in the MST

+A wrapper function which visualizes outputs from the 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")

@@ -27,9 +27,16 @@ A plot with the top genes that increase/decrease in expression with increasing p

 A wrapper function which visualizes outputs from the 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 <- singleCellTK::scaterlogNormCounts(sce, assayName = "logcounts")

+sce <- scater::runPCA(sce)

+sce <- scater::runTSNE (sce, dimred = "PCA")

 sce <- runTSCAN (inSCE = sce, useReducedDim = "PCA", seed = NULL)

-sce <- runTSCANDEG(inSCE = sce, pathIndex = 6, discardCluster = 8)

-plotTSCANPseudotimeGenes(inSCE = sce, pathIndex = 6, direction = "increasing")

+sce <- runTSCANDEG(inSCE = sce, pathIndex = 3)

+plotTSCANPseudotimeGenes(inSCE = sce, pathIndex = 3, direction = "increasing")

 }

 \author{

 Nida Pervaiz

@@ -27,9 +27,9 @@ A plot with the top genes that increase/decrease in expression with increasing p

 A wrapper function which visualizes outputs from the runTSCANDEG function. Plots the genes that increase or decrease in expression with increasing pseudotime along the path in the MST

 }

 \examples{

-sce <- runTSCAN (sce, useReducedDim = "PCA", seed = NULL)

-sce <- runTSCANDEG(sce, pathIndex = 6, discardCluster = 8)

-plotTSCANPseudotimeGenes(sce, pathIndex = 6, direction = "increasing")

+sce <- runTSCAN (inSCE = sce, useReducedDim = "PCA", seed = NULL)

+sce <- runTSCANDEG(inSCE = sce, pathIndex = 6, discardCluster = 8)

+plotTSCANPseudotimeGenes(inSCE = sce, pathIndex = 6, direction = "increasing")

 }

 \author{

 Nida Pervaiz

@@ -27,9 +27,9 @@ A plot with the top genes that increase/decrease in expression with increasing p

 A wrapper function which visualizes outputs from the runTSCANDEG function. Plots the genes that increase or decrease in expression with increasing pseudotime along the path in the MST

 }

 \examples{

-sce <- runTSCAN (sce, reducedDimName = "PCA", seed = NULL)

-sce <- runTSCANDEG(sce, pathIndex = 1, discardCluster = 8)

-plotTSCANPseudotimeGenes(sce, pathIndex = 1, direction = "increasing")

+sce <- runTSCAN (sce, useReducedDim = "PCA", seed = NULL)

+sce <- runTSCANDEG(sce, pathIndex = 6, discardCluster = 8)

+plotTSCANPseudotimeGenes(sce, pathIndex = 6, direction = "increasing")

 }

 \author{

 Nida Pervaiz

new file mode 100644

@@ -0,0 +1,36 @@

+% 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 number for which the pseudotime values should be used. PathIndex corresponds to one path from the root node to one of the terminal nodes.}

+

+\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 runTSCANDEG function. Plots the genes that increase or decrease in expression with increasing pseudotime along the path in the MST

+}

+\examples{

+sce <- runTSCAN (sce, reducedDimName = "PCA", seed = NULL)

+sce <- runTSCANDEG(sce, pathIndex = 1, discardCluster = 8)

+plotTSCANPseudotimeGenes(sce, pathIndex = 1, direction = "increasing")

+}

+\author{

+Nida Pervaiz

+}