@@ -37,8 +37,6 @@ Imports:

   mixtools,

   RColorBrewer,

   boot,

-  shiny,

-  miniUI,

   rhdf5,

   RUVSeq,

   DT,

@@ -50,9 +48,11 @@ Imports:

   rARPACK

 Suggests:

   BiocStyle,

-  scRNAseq,

   knitr,

+  miniUI,

   rmarkdown,

+  scRNAseq,

+  shiny,

   testthat

 VignetteBuilder: knitr

 LazyLoad: yes

@@ -93,9 +93,6 @@ importFrom(limma,lmFit)

 importFrom(matrixStats,colIQRs)

 importFrom(matrixStats,colMedians)

 importFrom(matrixStats,rowMedians)

-importFrom(miniUI,gadgetTitleBar)

-importFrom(miniUI,miniContentPanel)

-importFrom(miniUI,miniPage)

 importFrom(mixtools,normalmixEM)

 importFrom(rARPACK,svds)

 importFrom(reshape2,melt)

@@ -107,7 +104,6 @@ importFrom(rhdf5,h5write)

 importFrom(rhdf5,h5write.default)

 importFrom(scran,computeSumFactors)

 importFrom(shiny,br)

-importFrom(shiny,brushedPoints)

 importFrom(shiny,column)

 importFrom(shiny,downloadHandler)

 importFrom(shiny,downloadLink)

@@ -123,20 +119,16 @@ importFrom(shiny,plotOutput)

 importFrom(shiny,reactive)

 importFrom(shiny,renderPlot)

 importFrom(shiny,renderTable)

-importFrom(shiny,renderText)

-importFrom(shiny,runGadget)

 importFrom(shiny,selectInput)

 importFrom(shiny,shinyApp)

 importFrom(shiny,sidebarLayout)

 importFrom(shiny,sidebarPanel)

 importFrom(shiny,sliderInput)

-importFrom(shiny,stopApp)

 importFrom(shiny,tabPanel)

 importFrom(shiny,tableOutput)

 importFrom(shiny,tabsetPanel)

 importFrom(shiny,titlePanel)

 importFrom(shiny,updateSelectInput)

-importFrom(shiny,verbatimTextOutput)

 importFrom(stats,approx)

 importFrom(stats,as.formula)

 importFrom(stats,binomial)

@@ -1,24 +1,20 @@

 #' Interactive biplot

-#' 

+#'

 #' This is a wrapper around \code{\link{biplot_color}}, creating a shiny gadget

 #' to allow the user to select specific points in the graph.

-#' 

+#'

 #' @details Since this is based on the shiny gadget feature, it will not work

 #'   in static documents, such as vignettes or markdown / knitr documents. See

 #'   \code{biplot_color} for more details on the internals.

-#'   

+#'

 #' @param x a \code{\link{SconeExperiment}} object.

 #' @param ... passed to \code{\link{biplot_color}}.

-#'   

-#' @importFrom miniUI gadgetTitleBar miniContentPanel miniPage gadgetTitleBar

-#' @importFrom shiny plotOutput renderPlot observeEvent brushedPoints runGadget

-#'   verbatimTextOutput stopApp renderText

-#'   

+#'

 #' @export

-#' 

-#' @return A \code{\link{SconeExperiment}} object representing 

+#'

+#' @return A \code{\link{SconeExperiment}} object representing

 #'   selected methods.

-#'   

+#'

 #' @examples

 #' mat <- matrix(rpois(1000, lambda = 5), ncol=10)

 #' colnames(mat) <- paste("X", 1:ncol(mat), sep="")

@@ -30,19 +26,27 @@

 #' \dontrun{

 #' biplot_interactive(res)

 #' }

-#' 

+#'

 biplot_interactive <- function(x, ...) {

+  if (!requireNamespace("shiny", quietly = TRUE)) {

+    stop("shiny package needed for biplot_interactive")

+  }

+

+  if (!requireNamespace("miniUI", quietly = TRUE)) {

+    stop("miniUI package needed for biplot_interactive")

+  }

+

   data <- as.data.frame(apply(t(get_scores(x)),1,rank))

   scores <- get_score_ranks(x)

-  ui <- miniPage(

-    gadgetTitleBar("Drag to select points"),

-    miniContentPanel(

+  ui <- miniUI::miniPage(

+    miniUI::gadgetTitleBar("Drag to select points"),

+    miniUI::miniContentPanel(

       # The brush="brush" argument means we can listen for

       # brush events on the plot using input$brush.

-      plotOutput("plot1", height = "80%", brush = "plot_brush"),

-      verbatimTextOutput("info")

+      shiny::plotOutput("plot1", height = "80%", brush = "plot_brush"),

+      shiny::verbatimTextOutput("info")

     )

   )

@@ -53,14 +57,14 @@ biplot_interactive <- function(x, ...) {

     bp_obj <- biplot_color(pc_obj, y = scores)

     # Render the plot

-    output$plot1 <- renderPlot({

+    output$plot1 <- shiny::renderPlot({

       # Biplot

       biplot_color(pc_obj, y = scores, ...)

     })

     data_out <- cbind(data, bp_obj)

-    output$info <- renderText({

+    output$info <- shiny::renderText({

       xy_range_str <- function(e) {

         if(is.null(e)) return("NULL\n")

         idx <- which(bp_obj[,1] >= e$xmin & bp_obj[,1] <= e$xmax &

@@ -71,16 +75,16 @@ biplot_interactive <- function(x, ...) {

     })

     # Handle the Done button being pressed.

-    observeEvent(input$done, {

+    shiny::observeEvent(input$done, {

       # Return the brushed points. See ?shiny::brushedPoints.

-      names <- rownames(brushedPoints(data_out, 

-                                      input$plot_brush, 

+      names <- rownames(shiny::brushedPoints(data_out,

+                                      input$plot_brush,

                                       xvar="PC1",

                                       yvar="PC2"))

       out <- select_methods(x, names)

-      stopApp(invisible(out))

+      shiny::stopApp(invisible(out))

     })

   }

-  runGadget(ui, server)

+  shiny::runGadget(ui, server)

 }

@@ -12,7 +12,7 @@ biplot_interactive(x, ...)

 \item{...}{passed to \code{\link{biplot_color}}.}

 }

 \value{

-A \code{\link{SconeExperiment}} object representing 

+A \code{\link{SconeExperiment}} object representing

   selected methods.

 }

 \description{