@@ -187,6 +187,7 @@ seuratICA <- function(inSCE, useAssay, reducedDimName = "seuratICA", nics = 20)

 #' @param inSCE (sce) object on which to compute and store jackstraw plot

 #' @param useAssay Assay containing scaled counts to use in JackStraw calculation.

 #' @param dims Number of components to test in Jackstraw. If \code{NULL}, then all components are used. Default \code{NULL}.

+#' @param externalReduction Pass DimReduc object if PCA/ICA computed through other libraries. Default \code{NULL}.

 #' @examples

 #' data(scExample, package = "singleCellTK")

 #' \dontrun{

@@ -198,8 +199,17 @@ seuratICA <- function(inSCE, useAssay, reducedDimName = "seuratICA", nics = 20)

 #' }

 #' @return Updated \code{SingleCellExperiment} object with jackstraw computations stored in it

 #' @export

-seuratComputeJackStraw <- function(inSCE, useAssay, dims = NULL) {

+seuratComputeJackStraw <- function(inSCE, useAssay, dims = NULL, externalReduction = NULL) {

   seuratObject <- convertSCEToSeurat(inSCE, scaledAssay = useAssay)

+  if(!is.null(externalReduction)){

+    seuratObject <- FindVariableFeatures(seuratObject)

+    seuratObject <- ScaleData(seuratObject)

+    seuratObject@reductions <- list(pca = externalReduction)

+    seuratObject@[email protected] <- seuratObject@[email protected][match(rownames(GetAssayData(seuratObject, assay = "RNA", slot = "scale.data")), rownames(seuratObject@[email protected])),]

+    seuratObject@commands$RunPCA.RNA <- seuratObject@commands$NormalizeData.RNA

+    seuratObject@commands$RunPCA.RNA@params$rev.pca <- FALSE

+    seuratObject@commands$RunPCA.RNA@params$weight.by.var <- TRUE

+    }

   if(is.null(seuratObject@reductions[["pca"]])) {

     stop("'seuratPCA' must be run before JackStraw can be computed.")

   }

@@ -216,6 +226,7 @@ seuratComputeJackStraw <- function(inSCE, useAssay, dims = NULL) {

 #' Computes the plot object for jackstraw plot from the pca slot in the input sce object

 #' @param inSCE (sce) object from which to compute the jackstraw plot (pca should be computed)

 #' @param dims Number of components to plot in Jackstraw. If \code{NULL}, then all components are plotted Default \code{NULL}.

+#' @param externalReduction Pass DimReduc object if PCA/ICA computed through other libraries. Default \code{NULL}.

 #' @examples

 #' data(scExample, package = "singleCellTK")

 #' \dontrun{

@@ -228,8 +239,11 @@ seuratComputeJackStraw <- function(inSCE, useAssay, dims = NULL) {

 #' }

 #' @return plot object

 #' @export

-seuratJackStrawPlot <- function(inSCE, dims = NULL) {

+seuratJackStrawPlot <- function(inSCE, dims = NULL, externalReduction = NULL) {

   seuratObject <- convertSCEToSeurat(inSCE)

+  if(!is.null(externalReduction)){

+    seuratObject@reductions <- list(pca = externalReduction)

+  }

   if(is.null(seuratObject@reductions[["pca"]])) {

     stop("'seuratPCA' must be run before JackStraw can be computed.")

   }

@@ -2105,8 +2105,18 @@ shinyServer(function(input, output, session) {

     #extra code added by irzam starts here:

+    redDim <- reducedDim(vals$counts, gsub(" ", "_", input$dimRedNameInput))

+    new_pca <- CreateDimReducObject(

+      embeddings = redDim, 

+      assay = "RNA",

+      loadings = attr(redDim, "rotation"),

+      stdev = as.numeric(attr(redDim, "percentVar")), 

+      key = "PC_")

+    

     removeTab(inputId = "dimRedPCAICA_plotTabset", target = "PCA Plot")

     removeTab(inputId = "dimRedPCAICA_plotTabset", target = "Elbow Plot")

+    removeTab(inputId = "dimRedPCAICA_plotTabset", target = "Heatmap Plot")

+    removeTab(inputId = "dimRedPCAICA_plotTabset", target = "JackStraw Plot")

     appendTab(inputId = "dimRedPCAICA_plotTabset", tabPanel(title = "PCA Plot",

                                                             panel(heading = "PCA Plot",

@@ -2130,13 +2140,7 @@ shinyServer(function(input, output, session) {

                                                           )

       ))

-      redDim <- reducedDim(vals$counts, gsub(" ", "_", input$dimRedNameInput))

       withProgress(message = "Generating Elbow Plot", max = 1, value = 1, {

-        new_pca <- CreateDimReducObject(

-          embeddings = redDim, 

-          assay = "RNA",

-          stdev = as.numeric(attr(redDim, "percentVar")), 

-          key = "PC_")

         output$plotDimRed_elbow <- renderPlotly({

           seuratElbowPlot(inSCE = vals$counts,

@@ -2177,12 +2181,6 @@ shinyServer(function(input, output, session) {

         ))

         withProgress(message = "Generating Heatmaps", max = 1, value = 1, {

-          new_pca <- CreateDimReducObject(

-            embeddings = redDim, 

-            assay = "RNA",

-            loadings = attr(redDim, "rotation"),

-            stdev = as.numeric(attr(redDim, "percentVar")), 

-            key = "PC_")

           vals$counts@metadata$seurat$heatmap_dimRed <- seuratComputeHeatmap(inSCE = vals$counts,

                                                                           useAssay = input$dimRedAssaySelect,

                                                                           useReduction = "pca",

@@ -2198,6 +2196,23 @@ shinyServer(function(input, output, session) {

                               labels = c("PC1", "PC2", "PC3", "PC4"))

           })

         })

+        

+          appendTab(inputId = "dimRedPCAICA_plotTabset", tabPanel(title = "JackStraw Plot",

+                                                              panel(heading = "JackStraw Plot",

+                                                                    plotlyOutput(outputId = "plot_jackstraw_dimRed")

+                                                              )

+          ))

+          

+          withProgress(message = "Generating JackStraw Plot", max = 1, value = 1, {

+            vals$counts <- seuratComputeJackStraw(inSCE = vals$counts,

+                                                  useAssay = input$dimRedAssaySelect,

+                                                  dims = 10,

+                                                  externalReduction = new_pca)

+            output$plot_jackstraw_dimRed <- renderPlotly({

+              plotly::ggplotly(seuratJackStrawPlot(inSCE = vals$counts,

+                                                   dims = 10))

+            })

+          })

   })

   observeEvent(input$runDimred_tsneUmap, {

@@ -5,7 +5,7 @@

 \title{seuratComputeJackStraw

 Compute jackstraw plot and store the computations in the input sce object}

 \usage{

-seuratComputeJackStraw(inSCE, useAssay, dims = NULL)

+seuratComputeJackStraw(inSCE, useAssay, dims = NULL, externalReduction = NULL)

 }

 \arguments{

 \item{inSCE}{(sce) object on which to compute and store jackstraw plot}

@@ -13,6 +13,8 @@ seuratComputeJackStraw(inSCE, useAssay, dims = NULL)

 \item{useAssay}{Assay containing scaled counts to use in JackStraw calculation.}

 \item{dims}{Number of components to test in Jackstraw. If \code{NULL}, then all components are used. Default \code{NULL}.}

+

+\item{externalReduction}{Pass DimReduc object if PCA/ICA computed through other libraries. Default \code{NULL}.}

 }

 \value{

 Updated \code{SingleCellExperiment} object with jackstraw computations stored in it

@@ -5,12 +5,14 @@

 \title{seuratJackStrawPlot

 Computes the plot object for jackstraw plot from the pca slot in the input sce object}

 \usage{

-seuratJackStrawPlot(inSCE, dims = NULL)

+seuratJackStrawPlot(inSCE, dims = NULL, externalReduction = NULL)

 }

 \arguments{

 \item{inSCE}{(sce) object from which to compute the jackstraw plot (pca should be computed)}

 \item{dims}{Number of components to plot in Jackstraw. If \code{NULL}, then all components are plotted Default \code{NULL}.}

+

+\item{externalReduction}{Pass DimReduc object if PCA/ICA computed through other libraries. Default \code{NULL}.}

 }

 \value{

 plot object