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Question: I am trying to plot from a check box for fcs file in a reactive environment
0
gravatar for ramsnvenkat
9 weeks ago by
ramsnvenkat0 wrote:

my ui code is

    

rm(list = ls())

library(shiny)
library(flowCore)


shinyUI(fluidPage(
  titlePanel("Quality Control for Flow Cytometry Data"),
  
  fluidRow(
    column(3,
           fileInput('fcsFiles', strong('Choose fcs file(s):'), multiple = TRUE, 
                     accept = c('text/fcs', '.fcs')),
           
           actionButton("goButton", "Submit!"),
           hr(),
           
           
           ## sample limits: 50
           uiOutput("sample_select"),
           
           lapply(1:50, function(i) {
             uiOutput(paste0('timeSlider', i))
          }),
           
           hr(),
           uiOutput(outputId= "marker_select"),
         
          uiOutput(outputId= "marker_select121"),
           hr()
          
          
    ),
  
  
 sidebarPanel(
  
   
  numericInput("num1", label = h6("WBC COUNT"), value = 1,min = 0, max = NA, step = NA),
  
  hr(),
  fluidRow(column(3, verbatimTextOutput("wbc"))),
  
  numericInput("num2", label = h6("lymphocyte percentage"), value = 1,min = 0, max = NA, step = NA),
  
  hr(),
  
  fluidRow(column(3, verbatimTextOutput("lymphocyte"))),
 
  textOutput("ablymph"),
  uiOutput(outputId= "xaxis"),
  hr(),
  uiOutput(outputId= "yaxis"),
  hr(),
 
  actionButton("goButton", "Submit!")
 ),
    mainPanel(
      plotOutput("fowardside"),
    
      plotOutput("cd3plot"),
      plotOutput("cd4plot"),
      plotOutput("meplot"),
      plotOutput("cd8plot")
      
    )
  )
))

and my server.r code is

r

rm(list = ls())


library(flowCore)
library(shiny)
library(flowViz)
library(flowStats)

shinyServer(function(input, output,session) {
  
  output$ablymph <- renderText({
    W <- input$num1
    L <- input$num2
    x <- W*(L/100)
    paste("Absolute Lymphocytes Count is =", x)
  })
  
  set <- reactive({
    if (input$goButton == 0)
      return()
    isolate({fcsFiles<- input$fcsFiles
    if (is.null(fcsFiles))
      return (NULL)
    set <- read.flowSet(fcsFiles$datapath)
    sampleNames(set)<- fcsFiles$name})
    return(set)
    print(set)
  })
  
  
  output$sample_select <- renderUI({
    if(is.null(set())){
      return(NULL)
    }else{
      
      checkboxGroupInput('samples', strong('Select samples:'), 
                         sampleNames(set()), selected = sampleNames(set()))
    }   
  }) 
  markerNames <- reactive({
    if(is.null(set()))
      return(NULL)
    pd <- set()[[1]]@parameters@data
    markers <- paste("<", pd$name, ">:", pd$desc, sep = "")
    return(markers)
  })
  
  output$marker_select <- renderUI({
    if(is.null(markerNames())){
      return(NULL)
    }else{
      radioButtons(inputId = 'paras', label = ('Select markers for X-AXIS:'), 
                         choices =  markerNames(), selected = )
    }   
    
  })
    
  output$marker_select121 <- renderUI({
    if(is.null(markerNames())){
      return(NULL)
    }else{
      radioButtons(inputId = 'paras1', label = ('Select markers for Y-AXIS:'), 
                         choices =  markerNames(), selected = NULL)
    }   
   
  
  })
  output$filetable <- renderTable({
    data1<- set()[[1]]@parameters@data
    return(data1)
  })
  output$cd3plot<-renderPlot({
    plot(set()[[1]]@parameters@data1[paras],set()[[1]]@parameters@data1[paras1])
   
     
  })
   
  })

 

i am not able to fine out how do I plot the different check box values are stores and plot them, can any one please help me. I am trying to learn it for my project. thanks in advance

ver code is 

 

 

R
ADD COMMENTlink modified 9 weeks ago by James W. MacDonald43k • written 9 weeks ago by ramsnvenkat0
0
gravatar for James W. MacDonald
9 weeks ago by
United States
James W. MacDonald43k wrote:

Shiny isn't a Bioconductor package, so this isn't the correct support forum for your question. I presume that the RStudio folks have some sort of listserv or whatnot that you could use, or perhaps you could try stackoverflow.

ADD COMMENTlink written 9 weeks ago by James W. MacDonald43k
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