include a glimma interface in a shiny app

Question

I am trying to code a shiny app for RNA-Seq data analysis.

I would like to include glimma interactive plots in it. However, in my current interface, clicking the action button Glimma plot opens the glimma interface in a new page of my web browser and not in the shiny UI.

I use shiny, glimma and EdgeR. Here is my code:

ui <- fluidPage(
  actionButton(inputId="run.glimma", label="Glimma plot"),
  htmlOutput("glimma")


server <- function(input, output, session){
  observeEvent(input$run.glimma, {
    glMDSPlot(dgeObj.norm(), labels=rownames(dgeObj.norm()$samples), groups=dgeObj.norm()$samples[,as.character(input$mds.grouping.feature)])
  }),

  output$glimma <- renderUI({
      includeHTML("glimma-plots/MDS-Plot.html")
    })
}

I only indicated the part of the code that I use to generate the glimma MDS plot.

Is there a way to display the glimma plots in the shiny app UI and not in a new webpage ?

Thank you

Answer 1

I have come across this page today with same query. After visiting here and there, finally following approach helped to resolve this issue. I must confess that I am just a beginner to R Shiny.

Lets say we have ui.R, server.R and global.R.

Inside global.R, add following code:

glimmaMDSOutput <- function(outputId, width = "100%", height = "400px") {
        htmlwidgets::shinyWidgetOutput(outputId, 'glimmaMDS', width, height, package = 'Glimma')
}

renderglimmaMDS <- function(expr, env = parent.frame(), quoted = FALSE) {
        if (!quoted) { expr <- substitute(expr) }
        htmlwidgets::shinyRenderWidget(expr, glimmaMDSOutput, env, quoted = TRUE)
}

Inside ui.R, add following:

glimmaMDSOutput(outputId = 'MDSplot')

**Inside server.R, add following:**
output$MDSplot <- renderglimmaMDS({
                Glimma::glimmaMDS(x = .., labels = .., groups = .., top = .., gene.selection = "pairwise", launch = FALSE, html = NULL, width = 1000, height = 500);
})