如何確定R腳本不工作的原因？

Question

我想運行這個文件並繪製基於該值，我也用ui.R腳本來打開文件。

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

shinyServer (function(input, output,server){ 
# trying to open a file 
ff <- input$file 
str(input$file) 
# to read a fcs file from a flow cytometer 
read.FCS("input$file", 
     transformation="linearize", 
     alter.names=FALSE, 
     column.pattern=NULL, 
     invert.pattern = FALSE, 
     decades=0, 
     ncdf=FALSE,      min.limit=NULL, 
     truncate_max_range = TRUE, 
     dataset=NULL, 
     emptyValue=TRUE) 

filedata <- reactive 
({ 
ff <- input$file 
str(input$file) 

       read.FCS("input$file", 
       transformation="linearize", 
       alter.names=FALSE, 
       column.pattern=NULL, 
       invert.pattern = FALSE, 
       decades=0, 
       ncdf=FALSE,      min.limit=NULL, 
       truncate_max_range = TRUE, 
       dataset=NULL, 
       emptyValue=TRUE) 
    output$distPlot <- renderPlot 
    ({ 
    lg <- rectangleGate("FS INT LIN"=c(350,700),"SS INT LIN"=c(50,250)) 

    lymp <- Subset(ff,lg) 
    # to compensate the values 
    bx<-biexponentialTransform() 
    bx1<-transformList(c("FL1 INT LOG","FL4 INT LOG"),bx) 
    bx2<-transformList(c("FL4 INT LOG","FL2 INT LOG"),bx) 
    bx3<-transformList(c("FL4 INT LOG","FL3 INT LOG"),bx) 
    CD45CD3<-transform(lymp,bx1) 
    CD3CD4<-transform(lymp,bx2) 
    CD3CD8<-transform(lymp,bx3) 

    # generate bins based on input$bins from ui.R 
    plot (ff, c("FS INT LIN","SS INT LIN"),xlim = c(100,1050),ylim=c(-10,900), 
    nbin=260) 
    xyplot(`SS INT LIN` ~ `FS INT LIN`,ff,filter=lg) 
    plot(lymp, c("FL1 INT LOG","FL2 INT LOG"),xlim = c(100,1050),ylim= 
    c(-10,900), nbin=260) 
    }) 
    # i want to run this app 
    }) 
    shinyApp(ui=ui,server=server) 
runApp("flowcyto", display.mode = "showcase") 
} 
) 

我曾嘗試使用我在這裏看到的幾篇文章，但似乎沒有工作。我正在努力重新創建一個基於流程細胞的自動化分析系統，第一步是調用文件並繪製相應的圖。 我得到的錯誤是：

Warning: Error in .getReactiveEnvironment()$currentContext: Operation not allowed without an active reactive context. (You tried to do something that can only be done from inside a reactive expression or observer.) 
Stack trace (innermost first): 
    46: .getReactiveEnvironment()$currentContext 
    45: .subset2(x, "impl")$get 
    44: $.reactivevalues 
    43: $ [C:\Users\ramaswamynathan.v\Desktop\r script\flowcyto/server.R#14] 
    42: server [C:\Users\ramaswamynathan.v\Desktop\r script\flowcyto/server.R#14] 
    1: runApp 
Error in .getReactiveEnvironment()$currentContext() : 
    Operation not allowed without an active reactive context. (You tried to do something that can only be done from inside a reactive expression or observer.) 

庫（閃亮）

# Define UI for application that draws a histogram 
shinyUI(fluidPage(

# Application title 
titlePanel("FLOW CYTOMETRY DATA"), 

titlePanel("Flow Cytometry"), 
# Upload File 
fileInput("file", label = h3("File input")), 

hr(), 
fluidRow(column(4, verbatimTextOutput("value"))) 

）） 我現在UI頁面只是從一個位置打開該文件，並用它來運行我的程序。

Answer 1

要確定爲什麼R腳本無法正常工作，只需要閱讀該錯誤或在瀏覽器中複製/粘貼，如果您真的不明白。

所以你的主要問題不應該是這個，你甚至不會說這是一個shiny問題，這是一個並非所有R用戶都知道的特定包。

對於你有光澤的問題，R是說你不尊重shiny的reactive的方法。事實上，有很多，我在這裏糾正錯誤的：

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

server <- shinyServer (function(input, output){ 
# trying to open a file  
filedata <- reactive 
({ 
ff <- input$file 
return(read.FCS("input$file", 
       transformation="linearize", 
       alter.names=FALSE, 
       column.pattern=NULL, 
       invert.pattern = FALSE, 
       decades=0, 
       ncdf=FALSE,      min.limit=NULL, 
       truncate_max_range = TRUE, 
       dataset=NULL, 
       emptyValue=TRUE))}) 
    output$distPlot <- renderPlot 
    ({ 
    lg <- rectangleGate("FS INT LIN"=c(350,700),"SS INT LIN"=c(50,250)) 

    lymp <- Subset(filedata(),lg) 
    # to compensate the values 
    bx<-biexponentialTransform() 
    bx1<-transformList(c("FL1 INT LOG","FL4 INT LOG"),bx) 
    bx2<-transformList(c("FL4 INT LOG","FL2 INT LOG"),bx) 
    bx3<-transformList(c("FL4 INT LOG","FL3 INT LOG"),bx) 
    CD45CD3<-transform(lymp,bx1) 
    CD3CD4<-transform(lymp,bx2) 
    CD3CD8<-transform(lymp,bx3) 

    # generate bins based on input$bins from ui.R 
    plot (filedata(), c("FS INT LIN","SS INT LIN"),xlim = c(100,1050),ylim=c(-10,900), 
    nbin=260) 
    xyplot(`SS INT LIN` ~ `FS INT LIN`,ff,filter=lg) 
    plot(lymp, c("FL1 INT LOG","FL2 INT LOG"),xlim = c(100,1050),ylim= 
    c(-10,900), nbin=260) 
    }) 
    # i want to run this app 
    }) 
     shinyApp(ui=ui,server=server) 

但問題是，有很多其他的混亂，我不能正確。例如在你的renderPlot你正在做三個地塊...

對於你的錯誤，你通過server在shinyServer這是絕對荒謬的。您還在reactive中包含renderPlot，您可以在服務器部分中撥打shinyApp。你甚至有一個ui部分？如果是的話，你應該把它添加到你的文章，因爲我想它包含錯誤。我不能確定修正是否詳盡，因爲如果沒有ui部分它不能被嘗試。

我強烈建議你看看shiny homepage。