Question

我在创建闪亮的应用程序方面是非常新的。需要一些帮助来解决错误。因此，我在文件final.csv中有如下数据：

structure(list(Samples = structure(c(1L, 12L, 23L, 34L, 45L, 
46L, 47L, 48L, 49L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 
13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 24L, 25L, 26L, 
27L, 28L, 29L, 30L, 31L, 32L, 33L, 35L, 36L, 37L, 38L, 39L, 40L, 
41L, 42L, 43L, 44L), .Label = c("Sample1", "Sample10", "Sample11", 
"Sample12", "Sample13", "Sample14", "Sample15", "Sample16", "Sample17", 
"Sample18", "Sample19", "Sample2", "Sample20", "Sample21", "Sample22", 
"Sample23", "Sample24", "Sample25", "Sample26", "Sample27", "Sample28", 
"Sample29", "Sample3", "Sample30", "Sample31", "Sample32", "Sample33", 
"Sample34", "Sample35", "Sample36", "Sample37", "Sample38", "Sample39", 
"Sample4", "Sample40", "Sample41", "Sample42", "Sample43", "Sample44", 
"Sample45", "Sample46", "Sample47", "Sample48", "Sample49", "Sample5", 
"Sample6", "Sample7", "Sample8", "Sample9"), class = "factor"), 
    years = c(1.301369863, 0.4, 1.054794521, 0.134246575, 0.794520548, 
    3.287671233, 3.646575342, 3.887671233, 3.646575342, 3.619178082, 
    3.575342466, 2.02739726, 3.523287671, 3.742465753, 2.926027397, 
    3.8, 1.161643836, 1.380821918, 3.087671233, 3.104109589, 
    3.084931507, 2.887671233, 2.778082192, 2.728767123, 3.043835616, 
    1.210958904, 2.704109589, 2.742465753, 2.635616438, 2.536986301, 
    2.432876712, 2.794520548, 1.967123288, 1.84109589, 1.838356164, 
    2.726027397, 2.430136986, 2.257534247, 1.876712329, 2.010958904, 
    0.698630137, 2.090410959, 2.098630137, 2.01369863, 1.717808219, 
    1.81369863, 2.057534247, 2.032876712, 1.989041096), patient.vital_status = c(0L, 
    0L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 
    1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L), A1BG = structure(c(1L, 1L, 2L, 2L, 1L, 2L, 2L, 
    1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 
    2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 
    1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L), .Label = c("high", 
    "low"), class = "factor"), A1CF = structure(c(1L, 1L, 1L, 
    1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 
    2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    2L), .Label = c("high", "low"), class = "factor")), class = "data.frame", row.names = c(NA, 
-49L))

使用以上信息，我正在尝试创建一个应用程序，但是在使其更正时遇到了一些麻烦。下面是我使用的代码：

library(shiny)
library(shinyjs)
library(tidyverse)
library(survminer)

ui <- fluidPage(
  titlePanel("survival"),
  sidebarLayout(
    sidebarPanel(
      selectInput(inputId = "thegene", label = "Gene", choices = c("A1BG", "A1CF"), selected = "A1CF"),
      radioButtons(inputId = "FileType", label = "Select the file type", choices = list("png", "pdf"), selected = "pdf"),
      width = 3
    ),
    mainPanel(
      plotOutput("plot"),
      downloadButton(outputId = "downloadPlot", label = "Download the plot"),
      width = 9
    )
  )
)

server <- function(input, output, session) {
  final <- read.csv("final.csv")
  genes <- as.factor(names(final[c(4:5)]))

  vals <- reactiveValues()

  alldat <- reactive({
    choices <- genes
    selected <- isolate(input$thegene)
    if (!selected %in% choices) selected <- choices[1]
    updateSelectInput(session, "thegene", choices = choices, selected = selected)
    final
  })

  dat <- reactive({
    x <- alldat()
    x[ x$variable == input$thegene,,drop=FALSE]
  })

  output$plot <- renderPlot({
      fit <- survfit(as.formula(paste0("Surv(years, patient.vital_status) ~", names(final[c(4:5)]))),
                     data = final)
      gg <-ggsurvplot(fit,
                 pval = TRUE, conf.int = FALSE,
                 risk.table = TRUE, # Add risk table
                 risk.table.col = "strata", # Change risk table color by groups
                 linetype = "strata", # Change line type by groups
                 surv.median.line = "hv", # Specify median survival
                 ggtheme = theme_bw(), # Change ggplot2 theme
                 palette = c("#FF0027", "#060606"),
                 xlim = c(0,10),
                 break.x.by = 3,
                 xlab="Time in years",
                 risk.table.y.text.col = T, # colour risk table text annotations.
                 risk.table.y.text = FALSE)
    vals$gg <- gg
    print(gg)
  })

  output$downloadPlot <- downloadHandler(
    filename =  function() {
      paste(input$thegene, input$FileType,sep=".")
    },
    # content is a function with argument file. content writes the plot to the device
    content = function(file){
      if(input$FileType=="png")
        png(file, units="in", width=5, height=5, res=300)
      else
        pdf(file, width = 5, height = 5, onefile = FALSE)
      print(vals$gg)
      dev.off()
    } 
  )
}

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

运行应用程序时使用上面的代码，我遇到了一个错误。

Error: object 'final' not found

我看到上面的错误，因此在运行应用程序之前，我加载了final.csv，还为genes分配了第4列和第5列的列名。然后，当我运行该应用程序时，它似乎正常工作，但是我只能看到A1BG基因输出。当我在界面中选择A1CF基因时，没有看到该输出，而是再次看到了A1BG的输出。

Answer 1

问题来自if中的alldata条件：您必须用if(!selected %in% choices)替换if (choices != NULL)，因为choices仅是NULL如果数据框final不存在（即未导入）。

您现在在survminer软件包中遇到了一些功能上的麻烦，但这是另一个问题，并且肯定是由于某些功能上的错字造成的。

Answer 2

该图未更新的原因是因为您使用names(final[c(4:5)]))作为survfit中的预测变量，而我认为您想使用input$thegene来代替。似乎按照预期的方式工作。

其他建议/注释：

您可能会避免将alldat更改为observe，而只是在final反应式中调用dat，因为您并没有以任何方式对其进行操作。首先反应。
应用程序似乎还有其他问题（例如survival软件包未显式加载，而"variable"名称中不存在final）。也许也值得一看。

R中闪亮的应用程序创建和输出问题

2 个答案: