如何修复R Shiny中的“错误:可变长度不同(为'input $ s'找到)" [英] how to fix 'Error: variable lengths differ (found for 'input$s')' in R Shiny

问题描述

我正在尝试制作一个简单的闪亮ap，以创建kaplan-meier生存曲线，并根据用户做出的选择对其进行分层.当我对KM计算进行静态编码(列名称为thorTr)时，它可以工作，但计算和绘图是静态的.当我用input $ s替换时，出现错误:可变长度不同(为"input $ s"找到)

I'm trying to make a simple shiny ap for creating kaplan-meier survival curves that are stratified by selection the user makes. When I code the KM calculation statically (with the column name thorTr) it works but the calculation and plot is static. When I replace with input$s I get ERROR:variable lengths differ (found for 'input$s')

我尝试查看其他使用as.formula并粘贴的代码，但我不理解，无法正常工作.但是我是R and Shiny的新用户，所以也许我做对了.这是一个类似的闪亮ap，但我想使用survminer和ggsurvplot进行绘图

I've tried looking at other code which use as.formula and paste, but I don't understand and couldn't get to work. But I am a new R and Shiny user so maybe I didn't get it right. Here is a similar shiny ap but I want to use survminer and the ggsurvplot for plotting

library(shiny)
library(ggplot2)
library(survival) 
library(survminer)

#load data
data(GBSG2, package = "TH.data")


#Define UI for application that plots stratified km curves
ui <- fluidPage(

  # Sidebar layout with a input and output definitions
  sidebarLayout(

    # Inputs
    sidebarPanel(

      # Select variable strat
      selectInput(inputId = "s", 
                  label = "Select Stratification Variable:",
                  choices = c("horTh","menostat","tgrade"), 
                  selected = "horTh")

    ),

    # Outputs
    mainPanel(
      plotOutput(outputId = "km")
    )
  )
)

# Define server function required to create the km plot
server <- function(input, output) {

  # Create the km plot object the plotOutput function is expecting
  output$km <- renderPlot({

    #calc KM estimate with a hard coded variables - the following line works but obviously is not reactive
    #km <- survfit(Surv(time,cens) ~ horTh,data=GBSG2)

    #replaced hard coded horTh selection with the respnse from the selection and I get an error
    km <- survfit(Surv(time,cens) ~ input$s ,data=GBSG2)

    #plot km
    ggsurvplot(km)

  })

}

# Create a Shiny app object
shinyApp(ui = ui, server = server)

我希望有一个可以根据用户选择来更新分层变量的图

I expect to have a plot that updates the stratification variable with the users selection

推荐答案

两件事:

1. survfit()调用中的公式需要明确定义.原始代码中传递给survfit()的对象使用函数右侧的字符值.这会引发错误，我们可以通过将整个粘贴的值转换为公式即as.formula(paste('Surv(time,cens) ~',input$s))
来解决.
2. 需要在对ggsurvplot()的调用中定义公式，以避免范围问题.这有点技术性，并且与ggsurvplot()的编程方式有关.基本上，ggsurvplot()不能访问在其自身调用之外定义的公式.

1. The formula in the call to survfit() needs to be defined explicitly. The object being passed to survfit() in the original code uses a character value on the right hand side of the function. This throws an error, which we can address by translating the entire pasted value into a formula, i.e., as.formula(paste('Surv(time,cens) ~',input$s))
2. The formula needs to be defined in the call to ggsurvplot() to avoid scoping issues. This is a little more technical and has to do with the way that ggsurvplot() is programmed. Basically, ggsurvplot() can't access a formula that is defined outside of its own call.

尝试更换

km <- survfit(Surv(time,cens) ~ input$s ,data=GBSG2)
ggsurvplot(km)

与

ggsurvplot(survfit(as.formula(paste('Surv(time,cens) ~',input$s)),data=GBSG2))

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