Download mixOmics figures in shiny app

Support
1

Hi,
I am developing a shiny app to analyze data using several mixOmics functions (plotIndiv, plotVar, plotLoadings). When I download the figures from the app, I am getting .htm files instead of the figures that are supposed to be png or pdf format. I noticed this issue with figures from mixOmics only. The other figures in the app from other libraries are downloaded successfully.

Thank you

2

Hi @muna59,

I have no issue downloading the plot as png. Here’s the app that I use:

library(shiny)
library(mixOmics)

# Define UI for application that draws a histogram
ui <- fluidPage(
    titlePanel("plotIndiv"),
    sidebarLayout(
        sidebarPanel(
            numericInput('pc1', 'First PC', value=1,
                         min=1, max=5, step=1),
            numericInput('pc2', 'Second PC', value=2,
                         min=1, max=5, step=1)
        ),
        mainPanel(plotOutput("plotIndiv"))
    )
)

server <- function(input, output) {

    output$plotIndiv <- renderPlot({
        data(multidrug)
        comp <- c(input$pc1, input$pc2)
        pca.res <- pca(multidrug$ABC.trans, ncomp = 5, scale = TRUE)
        # biplot(pca.res, group = multidrug$cell.line$Class, legend.title = 'Class')
        # samples representation
        plotIndiv(pca.res, comp = comp, ind.names = multidrug$cell.line$Class,
                  group = as.numeric(as.factor(multidrug$cell.line$Class)))
        
    })
}

# Run the application 
shinyApp(ui = ui, server = server)

I click on ‘Open in Browser’ and then I download it. Can you confirm you have any issues doing so with the app I provided?

Best,
Al

3

Thank you.
Actually, I need to download the plot in pdf format. For example, I tried to use the following code:

library(shiny)
library(mixOmics)

# Define UI for application that draws a histogram

ui <- fluidPage(
  titlePanel("plotIndiv"),
  sidebarLayout(  
    sidebarPanel(     
      numericInput('pc1', 'First PC', value=1,                   
                   min=1, max=5, step=1),     
      numericInput('pc2', 'Second PC', value=2,                  
                   min=1, max=5, step=1),
      downloadButton("Indiv_pdf", "Save as pdf")     
    ),    
    mainPanel(plotOutput("plotIndiv"))  
  )  
)

server <- function(input, output) {
  output$plotIndiv <- renderPlot({   
    data(multidrug)   
    comp <- c(input$pc1, input$pc2)   
    pca.res <- pca(multidrug$ABC.trans, ncomp = 5, scale = TRUE)   
    # biplot(pca.res, group = multidrug$cell.line$Class, legend.title = 'Class')   
    # samples representation   
    plotIndiv(pca.res, comp = comp, ind.names = multidrug$cell.line$Class,      
              group = as.numeric(as.factor(multidrug$cell.line$Class)))
  
  })
  output$Indiv_pdf <- downloadHandler(
    filename = function() {base::paste("pls_ind", ".pdf", sep = '')},
    content = function(file){
      ggsave(file, plot = plotIndiv, device = 'pdf')
    }
  )
  
}

# Run the application 
shinyApp(ui = ui, server = server)

It gives the following error: “Couldn’t download _ Server problem”.

4

Hi @muna59,

Please note that this is a Shiny support question and not a mixOmics one. Feel free to check online Shiny forums to get assistance (e.g. Problem in downloading the plot with downloadhandler for shiny app - shiny - RStudio Community).

Best,

Al