Hello,

I have created an interactive volcano plot using the Glimma glXY function which creates a glimma-plots folder locally in my working directory, within which contains the html file for the volcano plot. The volcano plot is quite nice and I would like to share it with collaborators who do not code and/or embed a link to the html file in a publication. What is the best way of doing this?

As per the Glimma package documentation, I have tried emailing the entire glimma-plots folder to collaborators but my email server blocks this.

Could RShiny be used for this purpose? If so, I would be very grateful if you could share some code you have used to create the ui and server for a Shiny App hosting an interactive Glimma plot. I see other users have had difficulty including Glimma plots in an RShiny interface (https://bioinformatics.stackexchange.com/questions/11101/include-a-glimma-interface-in-a-shiny-app).

Code for glXYplot:

glXYPlot(
      x = mbsham$log2FoldChange,
      y = -log10(mbsham$pvalue),
      xlab = "log2FC",
      ylab = "-log10pvalue (FDR)",
      main = "ZDSD MB vs SHAM",
      counts = counts,
      groups = groups$V2,
      samples = groups$V1,
      status = status,
      side.main = "SYMBOL",
      display.columns = c("ENTREZID", "ENSEMBL","SYMBOL", "NAME"),
      anno = anno,
      cols = cols,
      sample.cols = sample.cols,
      html = "ZDSD_MB_VS_SHAM_INTERACTIVE_VP"
    )

I tried embedding this in an RShiny app as follows but this continues to open the Glimma interactive html separately to the Shiny app:

UI

ui <- fluidPage(    

  titlePanel("RNA-Seq"),
    # Create a spot for the barplot
    mainPanel(
      plotOutput("XYplot")  
    )
)

Server

server <- function(input, output) {

  output$XYplot <- renderPlot({

    glXYPlot(
      x = mbsham$log2FoldChange,
      y = -log10(mbsham$pvalue),
      xlab = "log2FC",
      ylab = "-log10pvalue (FDR)",
      main = "ZDSD MB vs SHAM",
      counts = counts,
      groups = groups$V2,
      samples = groups$V1,
      status = status,
      side.main = "SYMBOL",
      display.columns = c("ENTREZID", "ENSEMBL","SYMBOL", "NAME"),
      anno = anno,
      cols = cols,
      sample.cols = sample.cols,
      html = "ZDSD_MB_VS_SHAM_INTERACTIVE_VP"
    )
  })
}

shinyApp(ui, server)

Thank you very much for your help. Any advice greatly appreciated.