Shiny Module: Downloading all plots into a single PDF

shiny
, , ,
1

Hello! I am working on moving my Shiny app to a module format. Currently, I can load a .fcs file, analyze it and output plots and a table. I now need to take the plot outputs from each ID and generate a single PDF. I have tried with and without the the ns labeling with the download server 'grid.arrange(ns(vals$plotSSC,vals$plotFL2))` but that didn't work. I think that keeping the download UI and server separate from the modules is correct, but I haven't found much literature to guild me.

Currently, if I click the download button it cannot find the vals function from the fcsGatingServer
Any help is much appreciated

Here is a simplified version of my code:

library(shiny)
library(flowCore)
library(flowMeans)
library(flowViz)
library(grid)

fcsGatingServer<-function(id){
  moduleServer(id, function(input, output, session) {
vals <- reactiveValues(plotSSC=NULL, plotFL2=NULL) 
 filePath<- reactive(input$file$datapath) 
 
  output$plotSSC <- renderPlot({ 
      
      myfcs <- read.FCS(paste(filePath()), alter.names=TRUE)
temp1<-as.data.frame(myfcsT)
      
      vals$plotSSC<-ggplot(data=temp1,aes(x=`FSC.A`,y=`SSC.A`)),  size=.5)+labs(title=("BDS77 Isotype"))+theme(plot.title = element_text(size = rel(0.8)))
      
 plot(myfcs[,c("FSC.A", "SSC.A")],pch=".",  xlab="FSC.A", ylab="SSC.A")

output$plotFL2 <- renderPlot({
    
    plot(myfcs[,c("FSC.A", "FL2.A")],pch=".",  xlab="FSC.A", ylab="PE")
######
downloadServer = function(input, output) {
   
  output$export = downloadHandler(
    filename = function() {"plots.pdf"},
    content = function(file) {
      pdf(file, onefile = TRUE)
      grid.arrange(ns(vals$plotSSC))
      dev.off()
    }
  )}
##############

fcsGatingUI<-function(id) {
  ns<-NS(id)
  
  sidebarLayout(
    sidebarPanel(
      fileInput(ns("file"), label =ns("File"), multiple = F, accept = ".FCS", buttonLabel ="Browse")
     
    ),
    mainPanel(
      splitLayout(cellWidths =c("50%","50%"), plotOutput(ns("plotSSC")), 
                  plotOutput(ns("plotFL2")))
    )
  )}


server <- function(input, output, session) {
  fcsGatingServer("BDS65 CD54")
  fcsGatingServer("BDS65 Isotype")
  downloadServer
}

ui <- fluidPage(
  downloadButton("export", label = "Generate report"),
  fcsGatingUI("BDS65 CD54"),
  fcsGatingUI("BDS65 Isotype")
)

  shinyApp(ui, server)
2

I'm trying to look at your example but I think you may have missed a few brackets/parentheses in your editing.

ggplot(data=temp1,aes(x=FSC.A,y=SSC.A)), size=.5)
Are there supposed to be two parentheses after the SSC.A`?

Also are you missing a }) for both of your renderPlot({ ? I must be going crazy as I can't find them. :slight_smile:

I just to make sure I'm not missing any details before I look at it in more detail.

3

Hi flowcyto,

You may be interested by IFCshiny package for interactive analysis of imaging and conventional flow cytometry(DISCLAIMER,I am the maintainer)

Nonetheless, here are some lines that may help:

library(shiny)
library(ggplot2)
library(flowCore)
library(grid)
library(gridExtra)

fcsGatingServer <- function(id) {
  moduleServer(
    id,
    function(input, output, session) {
      vals <- reactiveValues(plotSSC=NULL, plotFL2=NULL) 
      temp1 <- reactive({
        tryCatch({
          # as a reprex I used example fileS from flowCore package to mimic e.g.
          # a BDS65 CD54 or a BDS65 Isotype
          # in your app you will have to use input$file$datapath
          # In addition, channels in this file are not the same as what you may have in your own project
          # so you will have to modify the names accordingly
          if(id == "BDS65 CD54") {
            fcsFile <- system.file("extdata", "0877408774.B08", package="flowCore") #input$file$datapath
          } else {
            fcsFile <- system.file("extdata", "0877408774.E07", package="flowCore") #input$file$datapath
          }
          myfcs <- read.FCS(fcsFile, alter.names=TRUE)
          as.data.frame(exprs(myfcs))
        }, error = function(e) {
          stop("please input fcs file")
        })
      })
      
      output$plotSSC <- renderPlot({
        vals$plotSSC <- ggplot(data=temp1()) +
          geom_point(aes(x=`FSC.H`,y=`SSC.H`),size=.5) +
          labs(title=("FSC / SSC")) +
          theme(plot.title = element_text(size = rel(0.8)))
        # I don't really understand why you compute a ggplot and then use a base plot
        # plot(temp1()[,c("FSC.H", "SSC.H")],pch=".",  xlab="FSC.H", ylab="SSC.H")
        vals$plotSSC
      })
      output$plotFL2 <- renderPlot({
        vals$plotFL2 <- ggplot(data=temp1()) +
          geom_point(aes(x=`FSC.H`,y=`FL2.H`),size=.5) +
          labs(title=("FSC / FL2")) +
          theme(plot.title = element_text(size = rel(0.8)))
        # plot(temp1()[,c("FSC.H", "FL2.H")],pch=".",  xlab="FSC.H", ylab="FL2.H") # ylab="PE")
        vals$plotFL2
      })
      output$export <- downloadHandler(
        filename = function() {
          paste0("plot_",id,".pdf")
        },
        content = function(file) {
          g_tbl <- arrangeGrob(vals$plotSSC, vals$plotFL2,
                               nrow=1, ncol=2, respect = TRUE, heights = 1)
          ggsave(file, arrangeGrob(g_tbl), device = "pdf", width = 8.5, height = 11)
        }
      )
      vals
    }
  )
}

fcsGatingUI<-function(id) {
  ns<-NS(id)
  
  sidebarLayout(
    sidebarPanel(
      downloadButton(ns("export"), label = "Generate report"),
      fileInput(ns("file"), label ="File", multiple = FALSE, accept = ".FCS", buttonLabel ="Browse")
    ),
    mainPanel(
      splitLayout(cellWidths =c("50%","50%"),
                  plotOutput(ns("plotSSC")), 
                  plotOutput(ns("plotFL2")))
    )
  )
}


server <- function(input, output, session) {
  fcsGatingServer("BDS65 CD54")
  fcsGatingServer("BDS65 Isotype")
}

ui <- fluidPage(
  fcsGatingUI("BDS65 CD54"),
  fcsGatingUI("BDS65 Isotype")
)

shinyApp(ui, server)

EDIT:
I read too quickly...
You want a pdf with all the plots inside:

library(shiny)
library(ggplot2)
library(flowCore)
library(grid)
library(gridExtra)

fcsGatingServer <- function(id) {
  moduleServer(
    id,
    function(input, output, session) {
      vals <- reactiveValues(plotSSC=NULL, plotFL2=NULL) 
      temp1 <- reactive({
        tryCatch({
          # as a reprex I used example fileS from flowCore package to mimic e.g.
          # a BDS65 CD54 or a BDS65 Isotype
          # in your app you will have to use input$file$datapath
          # In addition, channels in this file are not the same as what you may have in your own project
          # so you will have to modify the names accordingly
          if(id == "BDS65 CD54") {
            fcsFile <- system.file("extdata", "0877408774.B08", package="flowCore") #input$file$datapath
          } else {
            fcsFile <- system.file("extdata", "0877408774.E07", package="flowCore") #input$file$datapath
          }
          myfcs <- read.FCS(fcsFile, alter.names=TRUE)
          as.data.frame(exprs(myfcs))
        }, error = function(e) {
          stop("please input fcs file")
        })
      })
      
      output$plotSSC <- renderPlot({
        vals$plotSSC <- ggplot(data=temp1()) +
          geom_point(aes(x=`FSC.H`,y=`SSC.H`),size=.5) +
          labs(title=("FSC / SSC")) +
          theme(plot.title = element_text(size = rel(0.8)))
        # I don't really understand why you compute a ggplot and then use a base plot
        # plot(temp1()[,c("FSC.H", "SSC.H")],pch=".",  xlab="FSC.H", ylab="SSC.H")
        vals$plotSSC
      })
      output$plotFL2 <- renderPlot({
        vals$plotFL2 <- ggplot(data=temp1()) +
          geom_point(aes(x=`FSC.H`,y=`FL2.H`),size=.5) +
          labs(title=("FSC / FL2")) +
          theme(plot.title = element_text(size = rel(0.8)))
        # plot(temp1()[,c("FSC.H", "FL2.H")],pch=".",  xlab="FSC.H", ylab="FL2.H") # ylab="PE")
        vals$plotFL2
      })
      vals
    }
  )
}

fcsGatingUI<-function(id) {
  ns<-NS(id)
  
  sidebarLayout(
    sidebarPanel(
      fileInput(ns("file"), label ="File", multiple = FALSE, accept = ".FCS", buttonLabel ="Browse")
    ),
    mainPanel(
      splitLayout(cellWidths =c("50%","50%"),
                  plotOutput(ns("plotSSC")), 
                  plotOutput(ns("plotFL2")))
    )
  )
}


server <- function(input, output, session) {
  v1 <- fcsGatingServer("BDS65 CD54")
  v2 <- fcsGatingServer("BDS65 Isotype")
  output$export <- downloadHandler(
    filename = function() {
      paste0("plot.pdf")
    },
    content = function(file) {
      g_tbl <- arrangeGrob(v1$plotSSC, v1$plotFL2,
                           v2$plotSSC, v2$plotFL2,
                           nrow=2, ncol=2, respect = TRUE, heights = rep(1, 2))
      ggsave(file, arrangeGrob(g_tbl), device = "pdf", width = 8.5, height = 11)
    }
  )
}

ui <- fluidPage(
  fcsGatingUI("BDS65 CD54"),
  fcsGatingUI("BDS65 Isotype"),
  downloadButton("export", label = "Generate report")
)

shinyApp(ui, server)
4

Sorry! I took out a lot of code to try and make everything easier to follow and definitely deleted to many })'s. you are not going crazy. I should have double checked the the parentheses before posting

5

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